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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, Yigang 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 Sélem-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, Cecheng Zhao, Kun Yang, Dongyang Wang, Jiajun Yang, Xiaohui Niu, Jing Gong:
Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation. D659-D667 - Justine Dardaillon, Delphine Dauga, Paul Simion, Emmanuel Faure, Takeshi A. Onuma, Melissa B. DeBiasse, Alexandra Louis, Kazuhiro R. Nitta, Magali Naville, Lydia Besnardeau, Wendy Reeves, Kai Wang, Marie Fagotto, Marion Guéroult-Bellone, Shigeki Fujiwara, Rémi Dumollard, Michael Veeman, Jean-Nicolas Volff, Hugues Roest Crollius, Emmanuel J. P. Douzery, Joseph F. Ryan, Bradley Davidson, Hiroki Nishida, Christelle Dantec, Patrick Lemaire:
ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates. D668-D675 - Md. Shamimuzzaman, Justin J. Le Tourneau, Deepak R. Unni, Colin M. Diesh, Deborah A. Triant, Amy T. Walsh, Aditi Tayal, Gavin C. Conant, Darren E. Hagen, Christine G. Elsik:
Bovine Genome Database: new annotation tools for a new reference genome. D676-D681 - Andrew D. Yates, Premanand Achuthan, Wasiu A. Akanni, James E. Allen, Jamie Allen, Jorge Álvarez-Jarreta, M. Ridwan Amode, Irina M. Armean, Andrey G. Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, José Carlos Marugán, Carla A. Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Reham Fatima, Astrid Gall, Carlos García-Girón, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike P. Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, Thomas Maurel, Mark D. McDowall, Aoife McMahon, Shamika Mohanan, Benjamin Moore, Michael Nuhn, Denye N. Oheh, Anne Parker, Andrew Parton, Mateus Patricio, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, Mira Sycheva, Marek Szuba, Kieron R. Taylor, Anja Thormann, Glen Threadgold, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Bethany Flint, Adam Frankish, Sarah E. Hunt, Garth IIsley, Myrto Kostadima, Nick Langridge, Jane E. Loveland, Fergal J. Martin, Joannella Morales, Jonathan M. Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, Stephen J. Trevanion, Fiona Cunningham, Kevin L. Howe, Daniel R. Zerbino, Paul Flicek:
Ensembl 2020. D682-D688 - Kevin L. Howe, Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu A. Akanni, James E. Allen, Jorge Álvarez-Jarreta, Matthieu Barba, Dan M. Bolser, Lahcen Cambell, Manuel Carbajo, Marc Chakiachvili, Mikkel B. Christensen, Carla A. Cummins, Alayne Cuzick, Paul Davis, Silvie Fexova, Astrid Gall, Nancy George, Laurent Gil, Parul Gupta, Kim E. Hammond-Kosack, Erin Haskell, Sarah E. Hunt, Pankaj Jaiswal, Sophie H. Janacek, Paul J. Kersey, Nick Langridge, Uma Maheswari, Thomas Maurel, Mark D. McDowall, Benjamin Moore, Matthieu Muffato, Guy Naamati, Sushma Naithani, Andrew Olson, Irene Papatheodorou, Mateus Patricio, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Marc Rosello, Matthew Russell, Vasily Sitnik, Daniel M. Staines, Joshua C. Stein, Marcela K. Tello-Ruiz, Stephen J. Trevanion, Martin Urban, Sharon Wei, Doreen Ware, Gary Williams, Andrew D. Yates, Paul Flicek:
Ensembl Genomes 2020 - enabling non-vertebrate genomic research. D689-D695 - Virginie Courtier-Orgogozo, Laurent Arnoult, Stéphane R. Prigent, Séverine Wiltgen, Arnaud Martin:
Gephebase, a database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes. D696-D703 - Kent A. Shefchek, Nomi L. Harris, Michael A. Gargano, Nicolas Matentzoglu, Deepak R. Unni, Matthew H. Brush, Dan Keith, Tom Conlin, Nicole A. Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland:
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. D704-D715 - Molly A. Bogue, Vivek M. Philip, David O. Walton, Stephen C. Grubb, Matthew H. Dunn, Georgi Kolishovski, Jake Emerson, Gaurab Mukherjee, Tim Stearns, Hao He, Vinita Sinha, Beena Kadakkuzha, Kunde Ramamoorthy Govindarajan, Elissa J. Chesler:
Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data. D716-D723 - Param Priya Singh, Hervé Isambert:
OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates. D724-D730 - Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Stanley J. F. Laulederkind, Matthew J. Hoffman, Mary L. Kaldunski, Monika Tutaj, Jyothi Thota, Harika S. Nalabolu, Santoshi L. R. Ellanki, Marek Tutaj, Jeffrey DePons, Anne E. Kwitek, Melinda R. Dwinell, Mary Shimoyama:
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. D731-D742 - Patrick C. Ng, Edith D. Wong, Kevin A. MacPherson, Suzi A. Aleksander, Joanna Argasinska, Barbara Dunn, Robert S. Nash, Marek S. Skrzypek, Felix Gondwe, Sagar Jha, Kalpana Karra, Shuai Weng, Stuart R. Miyasato, Matt Simison, Stacia R. Engel, J. Michael Cherry:
Transcriptome visualization and data availability at the Saccharomyces Genome Database. D743-D748 - Lu Fang, Zhaoyuan Wei, Yongjiang Luo, Hailong Guo, Guoqing Zhang, Qingyou Xia, Yi Wang:
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm. D749-D755 - Christopher M. Lee, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Jairo Navarro Gonzalez, Angie S. Hinrichs, Brian T. Lee, Luis R. Nassar, Conner C. Powell, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Ann S. Zweig, David Haussler, Maximilian Haeussler, Robert M. Kuhn, W. James Kent:
UCSC Genome Browser enters 20th year. D756-D761 - Todd W. Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J. Chen, Jae-Hyoung Cho, Paul Davis, Sibyl Gao, Christian A. Grove, Ranjana Kishore, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, Paulo A. S. Nuin, Michael Paulini, Daniela Raciti, Faye Rodgers, Matthew Russell, Gary Schindelman, Kimberly Van Auken, Qinghua Wang, Gary Williams, Adam Wright, Karen Yook, Kevin L. Howe, Tim Schedl, Lincoln Stein, Paul W. Sternberg:
WormBase: a modern Model Organism Information Resource. D762-D767 - Qiao Wen Tan, Marek Mutwil:
Malaria.tools - comparative genomic and transcriptomic database for Plasmodium species. D768-D775 - Joshua D. Fortriede, Troy J. Pells, Stanley Chu, Praneet Chaturvedi, Dong Zhou Wang, Malcolm E. Fisher, Christina James-Zorn, Ying Wang, Mardi J. Nenni, Kevin A. Burns, Vaneet Lotay, Virgilio G. Ponferrada, Kamran Karimi, Aaron M. Zorn, Peter D. Vize:
Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database. D776-D782
Metabolic and Signaling Pathways
- Faviel F. Gonzalez-Galarza, Antony McCabe, Eduardo José Melo dos Santos, James Jones, Louise Y. C. Takeshita, Nestor D. Ortega-Rivera, Glenda M. Del Cid-Pavon, Kerry Ramsbottom, Gurpreet S. Ghattaoraya, Ana Alfirevic, Derek Middleton, Andrew R. Jones:
Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools. D783-D788 - Zhixiang Zuo, Huanjing Hu, Qingxian Xu, Xiaotong Luo, Di Peng, Kaiyu Zhu, Qi Zhao, Yubin Xie, Jian Ren:
BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers. D789-D796 - Chen Wang, Jian Yang, Hong Luo, Kun Wang, Yu Wang, Zhi-Xiong Xiao, Xiang Tao, Hao Jiang, Haoyang Cai:
CancerTracer: a curated database for intrapatient tumor heterogeneity. D797-D806 - Jianhua Wang, Dandan Huang, Yao Zhou, Hongcheng Yao, Huanhuan Liu, Sinan Zhai, Chengwei Wu, Zhanye Zheng, Ke Zhao, Zhao Wang, Xianfu Yi, Shijie Zhang, Xiaorong Liu, Zipeng Liu, Kexin Chen, Ying Yu, Pak Chung Sham, Mulin Jun Li:
CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies. D807-D816 - Ye Eun Jang, Insu Jang, Sunkyu Kim, Subin Cho, Daehan Kim, Keonwoo Kim, Jaewon Kim, Jimin Hwang, Sangok Kim, Jaesang Kim, Jaewoo Kang, Byungwook Lee, Sanghyuk Lee:
ChimerDB 4.0: an updated and expanded database of fusion genes. D817-D824 - Deepak Balamurali, Alessandro Gorohovski, Rajesh Detroja, Vikrant Palande, Dorith Raviv-Shay, Milana Frenkel-Morgenstern:
ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps. D825-D834 - Melissa J. Landrum, Shanmuga Chitipiralla, Garth R. Brown, Chao Chen, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang, Kuljeet Kaur, Chunlei Liu, Vitaly Lyoshin, Zenith Maddipatla, Rama Maiti, Joseph Mitchell, Nuala A. O'Leary, George R. Riley, Wenyao Shi, George Zhou, Valerie A. Schneider, Donna R. Maglott, J. Bradley Holmes, Brandi L. Kattman:
ClinVar: improvements to accessing data. D835-D844 - Janet Piñero González, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I. Furlong:
The DisGeNET knowledge platform for disease genomics: 2019 update. D845-D855 - Wubin Ding, Jiwei Chen, Guoshuang Feng, Geng Chen, Jun Wu, Yongli Guo, Xin Ni, Tieliu Shi:
DNMIVD: DNA methylation interactive visualization database. D856-D862 - Shu-Hsuan Liu, Pei-Chun Shen, Chen-Yang Chen, An-Ni Hsu, Yi-Chun Cho, Yo-Liang Lai, Fang-Hsin Chen, Chia-Yang Li, Shu-Chi Wang, Ming Chen, I-Fang Chung, Wei-Chung Cheng:
DriverDBv3: a multi-omics database for cancer driver gene research. D863-D870 - Hui Liu, Wenhao Zhang, Bo Zou, Jinxian Wang, Yuanyuan Deng, Lei Deng:
DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy. D871-D881 - Yunhai Luo, Benjamin C. Hitz, Idan Gabdank, Jason A. Hilton, Meenakshi S. Kagda, Bonita Lam, Zachary Myers, Paul Sud, Jennifer Jou, Khine Lin, Ulugbek K. Baymuradov, Keenan Graham, Casey Litton, Stuart R. Miyasato, J. Seth Strattan, Otto Jolanki, Jin-Wook Lee, Forrest Tanaka, Philip Adenekan, Emma O'Neill, J. Michael Cherry:
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. D882-D889 - Zhuang Xiong, Mengwei Li, Fei Yang, Yingke Ma, Jian Sang, Rujiao Li, Zhaohua Li, Zhang Zhang, Yiming Bao:
EWAS Data Hub: a resource of DNA methylation array data and metadata. D890-D895 - Pora Kim, Mengyuan Yang, Ke Yiya, Weiling Zhao, Xiaobo Zhou:
ExonSkipDB: functional annotation of exon skipping event in human. D896-D907 - Vanessa Neveu, Geneviève Nicolas, Reza M. Salek, David S. Wishart, Augustin Scalbert:
Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk. D908-D912 - Guihu Zhao, Kuokuo Li, Bin Li, Zheng Wang, Zhenghuan Fang, Xiaomeng Wang, Yi Zhang, Tengfei Luo, Qiao Zhou, Lin Wang, Yali Xie, Yijing Wang, Qian Chen, Lu Xia, Yu Tang, Beisha Tang, Kun Xia, Jinchen Li:
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. D913-D926 - Dongmei Tian, Pei Wang, Bixia Tang, Xufei Teng, Cuiping Li, Xiaonan Liu, Dong Zou, Shuhui Song, Zhang Zhang:
GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals. D927-D932 - Tim Beck, Tom Shorter, Anthony J. Brookes:
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. D933-D940 - Susan Fairley, Ernesto Lowy-Gallego, Emily Perry, Paul Flicek:
The International Genome Sample Resource (IGSR) collection of open human genomic variation resources. D941-D947 - James Robinson, Dominic J. Barker, Xenia Georgiou, Michael A. Cooper, Paul Flicek, Steven G. E. Marsh:
IPD-IMGT/HLA Database. D948-D955 - Jiang Li, Yawen Xue, Muhammad Talal Amin, Yanbo Yang, Jiajun Yang, Wen Zhang, Wenqian Yang, Xiaohui Niu, Hong-Yu Zhang, Jing Gong:
ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types. D956-D963 - William D. Lees, Christian E. Busse, Martin Corcoran, Mats Ohlin, Cathrine Scheepers, Frederick A. Matsen IV, Gur Yaari, Corey T. Watson, Andrew M. Collins, Adrian J. Shepherd:
OGRDB: a reference database of inferred immune receptor genes. D964-D970 - Yang Gao, Chao Zhang, Liyun Yuan, Yunchao Ling, Xiaoji Wang, Chang Liu, Yuwen Pan, Xiaoxi Zhang, Xixian Ma, Yuchen Wang, Yan Lu, Kai Yuan, Wei Ye, Jiaqiang Qian, Huidan Chang, Ruifang Cao, Xiao Yang, Ling Ma, Yuanhu Ju, Long Dai, Yuanyuan Tang, Guoqing Zhang, Shuhua Xu:
PGG.Han: the Han Chinese genome database and analysis platform. D971-D976 - Hong Sun, Yangfan Guo, Xiaoping Lan, Jia Jia, Xiaoshu Cai, Guoqing Zhang, Jingjing Xie, Qian Liang, Yixue Li, Guangjun Yu:
PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation. D977-D982 - Zhanye Zheng, Dandan Huang, Jianhua Wang, Ke Zhao, Yao Zhou, Zhenyang Guo, Sinan Zhai, Hang Xu, Hui Cui, Hongcheng Yao, Zhao Wang, Xianfu Yi, Shijie Zhang, Pak Chung Sham, Mulin Jun Li:
QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes. D983-D991 - Lionel Urán Landaburu, Ariel J. Berenstein, Santiago Videla, Parag Maru, Dhanasekaran Shanmugam, Ariel Chernomoretz, Fernán Agüero:
TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration. D992-D1005 - Jane F. Armstrong, Elena Faccenda, Simon D. Harding, Adam J. Pawson, Christopher Southan, Joanna L. Sharman, Brice Campo, David R. Cavanagh, Stephen P. H. Alexander, Anthony P. Davenport, Michael Spedding, Jamie A. Davies, NC-IUPHAR:
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. D1006-D1021 - Peilin Jia, Yulin Dai, Ruifeng Hu, Guangsheng Pei, Astrid Marilyn Manuel, Zhongming Zhao:
TSEA-DB: a trait?tissue association map for human complex traits and diseases. D1022-D1030 - Yunxia Wang, Song Zhang, Fengcheng Li, Ying Zhou, Ying Zhang, Zhengwen Wang, Runyuan Zhang, Jiang Zhu, Yuxiang Ren, Ying Tan, Chu Qin, Yinghong Li, Xiaoxu Li, Yuzong Chen, Feng Zhu:
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics. D1031-D1041 - Jiayi Yin, Wen Sun, Fengcheng Li, Jiajun Hong, Xiaoxu Li, Ying Zhou, Yinjing Lu, Mengzhi Liu, Xue Zhang, Na Chen, Xiuping Jin, Jia Xue, Su Zeng, Lushan Yu, Feng Zhu:
VARIDT 1.0: variability of drug transporter database. D1042-D1050 - Aviv Omer, Or Shemesh, Ayelet Peres, Pazit Polak, Adrian J. Shepherd, Corey T. Watson, Scott D. Boyd, Andrew M. Collins, William D. Lees, Gur Yaari:
VDJbase: an adaptive immune receptor genotype and haplotype database. D1051-D1056 - Dmitry V. Bagaev, Renske M. A. Vroomans, Jerome Samir, Ulrik Stervbo, Cristina Rius, Garry Dolton, Alexander Greenshields-Watson, Meriem Attaf, Evgeny S. Egorov, Ivan V. Zvyagin, Nina Babel, David K. Cole, Andrew J. Godkin, Andrew K. Sewell, Can Kesmir, Dmitry M. Chudakov, Fabio Luciani, Mikhail Shugay:
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. D1057-D1062
Human and Other Vertebrate Genomes
- Matteo Togninalli, Ümit Seren, Jan A. Freudenthal, J. Grey Monroe, Dazhe Meng, Magnus Nordborg, Detlef Weigel, Karsten M. Borgwardt, Arthur Korte, Dominik G. Grimm:
AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana. D1063-D1068 - Zhonghai Li, Yang Zhang, Dong Zou, Yi Zhao, Hou-Ling Wang, Yi Zhang, Xinli Xia, Jingchu Luo, Hongwei Guo, Zhang Zhang:
LSD 3.0: a comprehensive resource for the leaf senescence research community. D1069-D1075 - Dehe Wang, Weiliang Fan, Xiaolong Guo, Kai Wu, Siyu Zhou, Zonggui Chen, Danyang Li, Kun Wang, Yuxian Zhu, Yu Zhou:
MaGenDB: a functional genomics hub for Malvaceae plants. D1076-D1084 - Hua Peng, Kai Wang, Zhuo Chen, Yinghao Cao, Qiang Gao, Yan Li, Xiuxiu Li, Hongwei Lu, Huilong Du, Min Lu, Xin Yang, Chengzhi Liang:
MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. D1085-D1092 - Sushma Naithani, Parul Gupta, Justin Preece, Peter D'Eustachio, Justin Elser, Priyanka Garg, Daemon A. Dikeman, Jason Kiff, Justin Cook, Andrew Olson, Sharon Wei, Marcela K. Tello-Ruiz, Antonio Fabregat Mundo, Alfonso Muñoz-Pomer Fuentes, Suhaib Mohammed, Tiejun Cheng, Evan Bolton, Irene Papatheodorou, Lincoln Stein, Doreen Ware, Pankaj Jaiswal:
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. D1093-D1103 - Feng Tian, Dechang Yang, Yuqi Meng, Jinpu Jin, Ge Gao:
PlantRegMap: charting functional regulatory maps in plants. D1104-D1113 - Zhonglong Guo, Zheng Kuang, Ying Wang, Yongxin Zhao, Yihan Tao, Chen Cheng, Jing Yang, Xiayang Lu, Chen Hao, Tianxin Wang, Xiaoyan Cao, Jianhua Wei, Lei Li, Xiaozeng Yang:
PmiREN: a comprehensive encyclopedia of plant miRNAs. D1114-D1121
Human Genes and Diseases
- Bilal Nizami, Dorottya Bereczki-Szakál, Nikolett Varró, Kamal el Battioui, Vignesh U. Nagaraj, Imola Cs. Szigyártó, István Mándity, Tamás Beke-Somfai:
FoldamerDB: a database of peptidic foldamers. D1122-D1128 - Pawel Rubach, Sebastian Zajac, Borys Jastrzebski, Joanna I. Sulkowska, Piotr Sulkowski:
Genus for biomolecules. D1129-D1135 - Xinhao Shao, Isra N. Taha, Karl R. Clauser, Yu (Tom) Gao, Alexandra Naba:
MatrisomeDB: the ECM-protein knowledge database. D1136-D1144 - Eric W. Deutsch, Nuno Bandeira, Vagisha Sharma, Yasset Pérez-Riverol, Jeremy Carver, Deepti Jaiswal Kundu, David García-Seisdedos, Andrew F. Jarnuczak, Suresh Hewapathirana, Benjamin S. Pullman, Julie Wertz, Zhi Sun, Shin Kawano, Shujiro Okuda, Yu Watanabe, Henning Hermjakob, Brendan MacLean, Michael J. MacCoss, Yunping Zhu, Yasushi Ishihama, Juan Antonio Vizcaíno:
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. D1145-D1152 - Patroklos Samaras, Tobias Schmidt, Martin Frejno, Siegfried Gessulat, Maria Reinecke, Anna Jarzab, Jana Zecha, Julia Mergner, Piero Giansanti, Hans-Christian Ehrlich, Stephan Aiche, Johannes Rank, Harald Kienegger, Helmut Krcmar, Bernhard Küster, Mathias Wilhelm:
ProteomicsDB: a multi-omics and multi-organism resource for life science research. D1153-D1163 - Esteban Martínez-García, Ángel Goñi-Moreno, Bryan Bartley, James Alastair McLaughlin, Lucas Sánchez-Sampedro, Héctor Pascual del Pozo, Clara Prieto Hernández, Ada Serena Marletta, Davide De Lucrezia, Guzmán Sánchez-Fernández, Sofía Fraile, Víctor de Lorenzo:
SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts. D1164-D1170
- Jiayi Yin, Wen Sun, Feng Cheng Li, Jiajun Hong, Xiao Xu Li, Ying Zhou, Yinjing Lu, Mengzhi Liu, Xue Zhang, Na Chen, Xiuping Jin, Jia Xue, Su Zeng, Lushan Yu, Feng Zhu:
VARIDT 1.0: variability of drug transporter database (Corrigendum). D1171
Volume 48, Number Webserver-Issue, July 2020
- Editorial: the 18th annual Nucleic Acids Research web server issue 2020. W1-W4
- Rezarta Islamaj Dogan, Dongseop Kwon, Sun Kim, Zhiyong Lu:
TeamTat: a collaborative text annotation tool. W5-W11 - Julien Gobeill, Déborah Caucheteur, Pierre-André Michel, Luc Mottin, Emilie Pasche, Patrick Ruch:
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts. W12-W16 - Elliot D. Drew, Robert W. Janes:
PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures. W17-W24 - Shikai Jin, Vinícius G. Contessoto, Mingchen Chen, Nicholas P. Schafer, Wei Lu, Xun Chen, Carlos Bueno, Arya Hajitaheri, Brian J. Sirovetz, Aram Davtyan, Garegin A. Papoian, Min-Yeh Tsai, Peter G. Wolynes:
AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. W25-W30 - Markus Wiederstein, Manfred J. Sippl:
TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D. W31-W35 - Gabriele Orlando, Daniele Raimondi, Luciano Porto Kagami, Wim F. Vranken:
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values. W36-W40 - Fabrice Allain, Fabien Mareuil, Hervé Ménager, Michael Nilges, Benjamin Bardiaux:
ARIAweb: a server for automated NMR structure calculation. W41-W47 - Katrin Schöning-Stierand, Konrad Diedrich, Rainer Fährrolfes, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Ruben Steinegger, Matthias Rarey:
ProteinsPlus: interactive analysis of protein-ligand binding interfaces. W48-W53 - Eduardo Mayol, Adrián García-Recio, Johanna K. S. Tiemann, Peter W. Hildebrand, Ramon Guixà-González, Mireia Olivella, Arnau Cordomí:
HomolWat: a web server tool to incorporate 'homologous' water molecules into GPCR structures. W54-W59 - Zhanwen Li, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova, Adam Godzik:
FATCAT 2.0: towards a better understanding of the structural diversity of proteins. W60-W64 - Dmitry A. Suplatov, Yana A. Sharapova, Elizaveta Geraseva, Vytas K. Svedas:
Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies. W65-W71 - Vadim M. Gumerov, Igor B. Zhulin:
TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses. W72-W76 - Patryk Jarnot, Joanna Ziemska-Legiecka, Laszlo Dobson, Matthew Merski, Pablo Mier, Miguel A. Andrade-Navarro, John M. Hancock, Zsuzsanna Dosztányi, Lisanna Paladin, Marco Necci, Damiano Piovesan, Silvio C. E. Tosatto, Vasilis J. Promponas, Marcin Grynberg, Aleksandra Gruca:
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. W77-W84 - Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Fazel-Najafabadi, Wen Niu, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Jie Zheng, John Turner, Dusica Vidovic, Jake Jaffe, Michael J. MacCoss, Cathy Wu, Ajay Pillai, Avi Ma'ayan, Stephan C. Schürer, Michal Kouril, Mario Medvedovic, Jarek Meller:
piNET: a versatile web platform for downstream analysis and visualization of proteomics data. W85-W93 - Angelo Felline, Michele Seeber, Francesca Fanelli:
webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules. W94-W103 - Jirí Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomás Martínek, Jirí Damborský:
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. W104-W109 - Kristian Barrett, Cameron J. Hunt, Lene Lange, Anne S. Meyer:
Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes. W110-W115 - Zhen Wah Tan, Enrico Guarnera, Wei-Ven Tee, Igor N. Berezovsky:
AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations. W116-W124 - Yoochan Myung, Douglas E. V. Pires, David B. Ascher:
mmCSM-AB: guiding rational antibody engineering through multiple point mutations. W125-W131 - Sumaiya Iqbal, David Hoksza, Eduardo Pérez-Palma, Patrick May, Jakob B. Jespersen, Shehab S. Ahmed, Zaara T. Rifat, Henrike O. Heyne, Mohammad Sohel Rahman, Jeffrey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J. Campbell, Dennis Lal:
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. W132-W139 - Duolin Wang, Dongpeng Liu, Jiakang Yuchi, Fei He, Yuexu Jiang, Siteng Cai, Jingyi Li, Dong Xu:
MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization. W140-W146 - Douglas E. V. Pires, Carlos H. M. Rodrigues, David B. Ascher:
mCSM-membrane: predicting the effects of mutations on transmembrane proteins. W147-W153 - Nawar Malhis, Matthew Jacobson, Steven J. M. Jones, Jörg Gsponer:
LIST-S2: taxonomy based sorting of deleterious missense mutations across species. W154-W161 - Manuel Holtgrewe, Oliver Stolpe, Mikko Nieminen, Stefan Mundlos, Alexej Knaus, Uwe Kornak, Dominik Seelow, Lara Segebrecht, Malte Spielmann, Björn Fischer-Zirnsak, Felix Boschann, Ute Scholl, Nadja Ehmke, Dieter Beule:
VarFish: comprehensive DNA variant analysis for diagnostics and research. W162-W169 - Michal Wlasnowolski, Michal Sadowski, Tymon Czarnota, Karolina Jodkowska, Przemyslaw Szalaj, Zhonghui Tang, Yijun Ruan, Dariusz Plewczynski:
3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome. W170-W176 - Joachim Wolff, Leily Rabbani, Ralf Gilsbach, Gautier Richard, Thomas Manke, Rolf Backofen, Björn A. Grüning:
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. W177-W184 - Jorge Oscanoa, Lavanya Sivapalan, Emanuela Gadaleta, Abu Z. Dayem Ullah, Nicholas R. Lemoine, Claude Chelala:
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update). W185-W192 - Nina Baumgarten, Dennis Hecker, Sivarajan Karunanithi, Florian Schmidt, Markus List, Marcel H. Schulz:
EpiRegio: analysis and retrieval of regulatory elements linked to genes. W193-W199 - Simone Puccio, Giorgio Grillo, Arianna Consiglio, Maria Felicia Soluri, Daniele Sblattero, Diego Cotella, Claudio Santoro, Sabino Liuni, Gianluca De Bellis, Enrico Lugli, Clelia Peano, Flavio Licciulli:
InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data. W200-W207 - Clémentine Leporcq, Yannick G. Spill, Delphine Balaramane, Christophe Toussaint, Michaël Weber, Anaïs F. Bardet:
TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. W208-W217 - Qi Liu, Tanya Shvarts, Piotr Sliz, Richard I. Gregory:
RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution. W218-W229 - Lan Ke, Dechang Yang, Yu Wang, Yang Ding, Ge Gao:
AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse. W230-W238 - Anjali Garg, Neelja Singhal, Ravindra Kumar, Manish Kumar:
mRNALoc: a novel machine-learning based in-silico tool to predict mRNA subcellular localization. W239-W243 - Le Chang, Guangyan Zhou, Othman Soufan, Jianguo Xia:
miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology. W244-W251 - Pierre Giroux, Ricky Bhajun, Stéphane Segard, Claire Picquenot, Céline Charavay, Lise Desquilles, Guillaume Pinna, Christophe Ginestier, Josiane Denis, Nadia Cherradi, Laurent Guyon:
miRViz: a novel webserver application to visualize and interpret microRNA datasets. W252-W261 - Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Juan Antonio Marchal, Michael Hackenberg:
mirnaQC: a webserver for comparative quality control of miRNA-seq data. W262-W267 - Fabian Kern, Jérémy Amand, Ilya Senatorov, Alina Isakova, Christina Backes, Eckart Meese, Andreas Keller, Tobias Fehlmann:
miRSwitch: detecting microRNA arm shift and switch events. W268-W274 - Anjun Ma, Cankun Wang, Yuzhou Chang, Faith H. Brennan, Adam McDermaid, Bingqiang Liu, Chi Zhang, Phillip G. Popovich, Qin Ma:
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq. W275-W286 - Milad Miladi, Martin Raden, Sven Diederichs, Rolf Backofen:
MutaRNA: analysis and visualization of mutation-induced changes in RNA structure. W287-W291 - Tomasz K. Wirecki, Katarzyna Merdas, Agata Bernat, Michal J. Boniecki, Janusz M. Bujnicki, Filip Stefaniak:
RNAProbe: a web server for normalization and analysis of RNA structure probing data. W292-W299 - Jae Yeon Hwang, Sungbo Jung, Tae Lim Kook, Eric C. Rouchka, Jinwoong Bok, Juw Won Park:
rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. W300-W306 - Mattias Rydenfelt, Bertram Klinger, Martina Klünemann, Nils Blüthgen:
SPEED2: inferring upstream pathway activity from differential gene expression. W307-W312 - Pora Kim, Ke Yiya, Xiaobo Zhou:
FGviewer: an online visualization tool for functional features of human fusion genes. W313-W320 - Luís Q. Alves, Raquel Ruivo, Miguel M. Fonseca, Mónica Lopes-Marques, Pedro Ribeiro, Luís Filipe Castro:
PseudoChecker: an integrated online platform for gene inactivation inference. W321-W331 - Marco Passaro, Martina Martinovic, Valeria Bevilacqua, Elliot A. Hershberg, Grazisa Rossetti, Brian J. Beliveau, Raoul Jean Pierre Bonnal, Massimiliano Pagani:
OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment. W332-W339 - Roy Rabinowitz, Shiran Abadi, Shiri Almog, Daniel Offen:
Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing. W340-W347 - Jiawei Wang, Wei Dai, Jiahui Li, Ruopeng Xie, Rhys A. Dunstan, Christopher Stubenrauch, Yanju Zhang, Trevor Lithgow:
PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins. W348-W357 - Haidong Yi, Le Huang, Bowen Yang, Javi Gomez, Han Zhang, Yanbin Yin:
AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses. W358-W365 - Yifei Xu, Fan Yang-Turner, Denis Volk, Derrick W. Crook:
NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline. W366-W371 - Suluxan Mohanraj, Juan Javier Díaz-Mejía, Martin D. Pham, Hillary Elrick, Mia Husic, Shaikh Rashid, Ping Luo, Prabnur Bal, Kevin Lu, Samarth Patel, Alaina Mahalanabis, Alaine Naidas, Erik Christensen, Danielle Croucher, Laura M. Richards, Parisa Shooshtari, Michael Brudno, Arun K. Ramani, Trevor J. Pugh:
CReSCENT: CanceR Single Cell ExpressioN Toolkit. W372-W379 - Gaurhari Dass, Manh-Tu Vu, Pan Xu, Enrique Audain, Marc-Phillip Hitz, Björn A. Grüning, Henning Hermjakob, Yasset Pérez-Riverol:
The omics discovery REST interface. W380-W384 - Federico Taverna, Jermaine Goveia, Tobias K. Karakach, Shawez Khan, Katerina Rohlenova, Lucas Treps, Abhishek Subramanian, Luc Schoonjans, Mieke Dewerchin, Guy Eelen, Peter Carmeliet:
BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization. W385-W394 - Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel J. Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. W395-W402 - Fabrice P. A. David, Maria Litovchenko, Bart Deplancke, Vincent Gardeux:
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. W403-W414 - Wenlong Jia, Hechen Li, Shiying Li, Lingxi Chen, Shuai Cheng Li:
Oviz-Bio: a web-based platform for interactive cancer genomics data visualization. W415-W426 - Archana Hari, Daniel Lobo:
Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks. W427-W435 - Qingxia Yang, Yunxia Wang, Ying Zhang, Fengcheng Li, Weiqi Xia, Ying Zhou, Yunqing Qiu, Honglin Li, Feng Zhu:
NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data. W436-W448 - Birkir Reynisson, Bruno Alvarez, Sinu Paul, Bjoern Peters, Morten Nielsen:
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. W449-W454 - Sisira Kadambat Nair, Christopher Eeles, Chantal Ho, Gangesh Beri, Esther Yoo, Denis Tkachuk, Amy Tang, Parwaiz Nijrabi, Petr Smirnov, Heewon Seo, Danyel Jennen, Benjamin Haibe-Kains:
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. W455-W462 - Xiaoqing Guan, Meng Cai, Yang Du, Ence Yang, Jiafu Ji, Jianmin Wu:
CVCDAP: an integrated platform for molecular and clinical analysis of cancer virtual cohorts. W463-W471 - Alexandre Borrel, Scott S. Auerbach, Keith A. Houck, Nicole C. Kleinstreuer:
Tox21BodyMap: a webtool to map chemical effects on the human body. W472-W476 - Shaozhen Ding, Yu Tian, Pengli Cai, Dachuan Zhang, Xingxiang Cheng, Dandan Sun, Le Yuan, Junni Chen, Weizhong Tu, Dong-Qing Wei, Qian-Nan Hu:
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. W477-W487 - Aleksandr Ianevski, Anil K. Giri, Tero Aittokallio:
SynergyFinder 2.0: visual analytics of multi-drug combination synergies. W488-W493 - Heewon Seo, Denis Tkachuk, Chantal Ho, Anthony Mammoliti, Aria Rezaie, Seyed Ali Madani Tonekaboni, Benjamin Haibe-Kains:
SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology. W494-W501 - Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez:
PaccMann: a web service for interpretable anticancer compound sensitivity prediction. W502-W508 - Taiwen Li, Jingxin Fu, Zexian Zeng, David Cohen, Jing Li, Qianming Chen, Bo Li, Xiaole Shirley Liu:
TIMER2.0 for analysis of tumor-infiltrating immune cells. W509-W514 - Nico Gerstner, Tim Kehl, Kerstin Lenhof, Anne Müller, Carolin Mayer, Lea Eckhart, Nadja Liddy Grammes, Caroline Diener, Martin Hart, Oliver Hahn, Jörn Walter, Tony Wyss-Coray, Eckart Meese, Andreas Keller, Hans-Peter Lenhof:
GeneTrail 3: advanced high-throughput enrichment analysis. W515-W520 - Fabian Kern, Tobias Fehlmann, Jeffrey Solomon, Louisa Schwed, Nadja Liddy Grammes, Christina Backes, Kendall Van Keuren-Jensen, David W. Craig, Eckart Meese, Andreas Keller:
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems. W521-W528 - Long Tian, Chengjie Huang, Reza Mazloom, Lenwood S. Heath, Boris A. Vinatzer:
LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa. W529-W537 - Adrian M. Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M. Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José María Fernández, Laia Codó, The Quest for Orthologs Consortium, Josep Lluis Gelpí, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria Jesus Martin, Salvador Capella-Gutiérrez, Paul D. Thomas, Erik L. L. Sonnhammer, Christophe Dessimoz:
The Quest for Orthologs benchmark service and consensus calls in 2020. W538-W545 - Mehmet Direnç Mungan, Mohammad Alanjary, Kai Blin, Tilmann Weber, Marnix H. Medema, Nadine Ziemert:
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. W546-W552 - Uciel Chorostecki, Manuel Molina, Leszek P. Pryszcz, Toni Gabaldón:
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. W553-W557 - Elin Teppa, Diego J. Zea, Francesco Oteri, Alessandra Carbone:
COVTree: Coevolution in OVerlapped sequences by Tree analysis server. W558-W565 - John Lee, Manthan Shah, Sara Ballouz, Megan Crow, Jesse A. Gillis:
CoCoCoNet: conserved and comparative co-expression across a diverse set of species. W566-W571 - Sunil Nagpal, Rashmi Singh, Deepak Yadav, Sharmila S. Mande:
MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks. W572-W579 - Priyanka Banerjee, Mathias Dunkel, Emanuel Kemmler, Robert Preissner:
SuperCYPsPred - a web server for the prediction of cytochrome activity. W580-W585 - Alexandre Borrel, Kamel Mansouri, Sue Nolte, Trey Saddler, Mike Conway, Charles Schmitt, Nicole C. Kleinstreuer:
InterPred: a webtool to predict chemical autofluorescence and luminescence interference. W586-W590 - Tomás Racek, Ondrej Schindler, Dominik Tousek, Vladimír Horský, Karel Berka, Jaroslav Koca, Radka Svobodová Vareková:
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. W591-W596 - Xiaoyu Ge, Vineet K. Raghu, Panos K. Chrysanthis, Panayiotis V. Benos:
CausalMGM: an interactive web-based causal discovery tool. W597-W602
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