Nucleic Acids Research, Volume 46
Volume 46, Number Database-Issue, January 2018
Editorial
Database Resources
Nucleic acid sequence, structure, and regulation
Nicole Silvester,
Blaise T. F. Alako,
Clara Amid,
Ana Cerdeño-Tárraga,
Laura Clarke,
Iain Cleland,
Peter W. Harrison,
Suran Jayathilaka,
Simon Kay,
Thomas M. Keane,
Rasko Leinonen,
Xin Liu,
Josué Martínez-Villacorta,
Manuela Menchi,
Kethi Reddy,
Nima Pakseresht,
Jeena Rajan,
Marc Rossello,
Dmitriy Smirnov,
Ana Luisa Toribio,
Daniel Vaughan,
Vadim Zalunin,
Guy Cochrane:
The European Nucleotide Archive in 2017. D36-D40 Xianfeng Li,
Leisheng Shi,
Kun Zhang,
Wenqing Wei,
Qi Liu,
Fengbiao Mao,
Jinchen Li,
Wanshi Cai,
Huiqian Chen,
Huajing Teng,
Jiada Li,
Zhongsheng Sun:
CirGRDB: a database for the genome-wide deciphering circadian genes and regulators. D64-D70 Guanxiong Zhang,
Jian Shi,
Shiwei Zhu,
Yujia Lan,
Liwen Xu,
Huating Yuan,
Gaoming Liao,
Xiaoqin Liu,
Yunpeng Zhang,
Yun Xiao,
Xia Li:
DiseaseEnhancer: a resource of human disease-associated enhancer catalog. D78-D84 Bailing Zhou,
Huiying Zhao,
Jia-Feng Yu,
Chengang Guo,
Xianghua Dou,
Feng Song,
Guodong Hu,
Zanxia Cao,
Yuanxu Qu,
Yuedong Yang,
Yaoqi Zhou,
Jihua Wang:
EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments. D100-D105 Shengli Li,
Yuchen Li,
Bing Chen,
Jingjing Zhao,
Shulin Yu,
Yan Tang,
Qiupeng Zheng,
Yan Li,
Peng Wang,
Xianghuo He,
Shenglin Huang:
exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes. D106-D112 Jian Sang,
Zhennan Wang,
Man Li,
Jiabao Cao,
Guangyi Niu,
Lin Xia,
Dong Zou,
Fan Wang,
Xingjian Xu,
Xiaojiao Han,
Jinqi Fan,
Ye Yang,
Wanzhu Zuo,
Yang Zhang,
Wenming Zhao,
Yiming Bao,
Jing-Fa Xiao,
Songnian Hu,
Lili Hao,
Zhang Zhang:
ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. D121-D126 Hui Zhi,
Xin Li,
Peng Wang,
Yue Gao,
Baoqing Gao,
Dianshuang Zhou,
Yan Zhang,
Maoni Guo,
Ming Yue,
Weitao Shen,
Shangwei Ning,
Lianhong Jin,
Xia Li:
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease. D133-D138 Ming Yue,
Dianshuang Zhou,
Hui Zhi,
Peng Wang,
Yan Zhang,
Yue Gao,
Maoni Guo,
Xin Li,
Yanxia Wang,
Yunpeng Zhang,
Shangwei Ning,
Xia Li:
MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases. D181-D185 Pietro Boccaletto,
Marcin Magnus,
Catarina Almeida,
Adriana Zyla,
Astha Astha,
Radoslaw Pluta,
Blazej Baginski,
Elzbieta Jankowska,
Stanislaw Dunin-Horkawicz,
Tomasz Wirecki,
Michal Boniecki,
Filip Stefaniak,
Janusz M. Bujnicki:
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information. D202-D205 Shashikant Pujar,
Nuala A. O'Leary,
Catherine M. Farrell,
Jane Loveland,
Jonathan M. Mudge,
Craig Wallin,
Carlos García-Girón,
Mark Diekhans,
If Barnes,
Ruth Bennett,
Andrew E. Berry,
Eric Cox,
Claire Davidson,
Tamara Goldfarb,
Jose M. Gonzalez,
Toby Hunt,
John Jackson,
Vinita S. Joardar,
Mike P. Kay,
Vamsi K. Kodali,
Fergal J. Martin,
Monica McAndrews,
Kelly M. McGarvey,
Michael R. Murphy,
Bhanu Rajput,
Sanjida H. Rangwala,
Lillian D. Riddick,
Ruth L. Seal,
Marie-Marthe Suner,
David Webb,
Sophia Zhu,
Bronwen L. Aken,
Elspeth A. Bruford,
Carol J. Bult,
Adam Frankish,
Terence D. Murphy,
Kim D. Pruitt:
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. D221-D228 Ayako Suzuki,
Shin Kawano,
Toutai Mituyama,
Mikita Suyama,
Yae Kanai,
Katsuhiko Shirahige,
Hiroyuki Sasaki,
Katsushi Tokunaga,
Katsuya Tsuchihara,
Sumio Sugano,
Kenta Nakai,
Yutaka Suzuki:
DBTSS/DBKERO for integrated analysis of transcriptional regulation. D229-D238 Dimitra Karagkouni,
Maria D. Paraskevopoulou,
Serafeim Chatzopoulos,
Ioannis S. Vlachos,
Spyros Tastsoglou,
Ilias Kanellos,
Dimitris Papadimitriou,
Ioannis Kavakiotis,
Sofia Maniou,
Giorgos Skoufos,
Thanasis Vergoulis,
Theodore Dalamagas,
Artemis G. Hatzigeorgiou:
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. D239-D245 Irene Papatheodorou,
Nuno A. Fonseca,
Maria Keays,
Y. Amy Tang,
Elisabet Barrera,
Wojciech Bazant,
Melissa Burke,
Anja Füllgrabe,
Alfonso Muñoz-Pomer Fuentes,
Nancy George,
Laura Huerta,
Satu Koskinen,
Suhaib Mohammed,
Matthew J. Geniza,
Justin Preece,
Pankaj Jaiswal,
Andrew Jarnuczak,
Wolfgang Huber,
Oliver Stegle,
Juan Antonio Vizcaíno,
Alvis Brazma,
Robert Petryszak:
Expression Atlas: gene and protein expression across multiple studies and organisms. D246-D251 Ivan V. Kulakovskiy,
Ilya E. Vorontsov,
Ivan S. Yevshin,
Ruslan N. Sharipov,
Alla D. Fedorova,
Eugene I. Rumynskiy,
Yulia A. Medvedeva,
Arturo Magana-Mora,
Vladimir B. Bajic,
Dmitri A. Papatsenko,
Fedor A. Kolpakov,
Vsevolod J. Makeev:
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. D252-D259 Aziz Khan,
Oriol Fornes,
Arnaud Stigliani,
Marius Gheorghe,
Jaime Abraham Castro-Mondragón,
Robin van der Lee,
Adrien Bessy,
Jeanne Chèneby,
Shubhada R. Kulkarni,
Ge Tan,
Damir Baranasic,
David J. Arenillas,
Albin Sandelin,
Klaas Vandepoele,
Boris Lenhard,
Benoît Ballester,
Wyeth W. Wasserman,
François Parcy,
Anthony Mathelier:
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. D260-D266 Hui Liu,
Huaizhi Wang,
Zhen Wei,
Songyao Zhang,
Gang Hua,
Shao-Wu Zhang,
Lin Zhang,
Shou-Jiang Gao,
Jia Meng,
Xing Chen,
Yufei Huang:
MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. D281-D287 Chih-Hung Chou,
Sirjana Shrestha,
Chi-Dung Yang,
Nai-Wen Chang,
Yu-Ling Lin,
Kuang-Wen Liao,
Wei-Chih Huang,
Ting-Hsuan Sun,
Siang-Jyun Tu,
Wei-Hsiang Lee,
Men-Yee Chiew,
Chun-San Tai,
Ting-Yen Wei,
Tzi-Ren Tsai,
Hsin-Tzu Huang,
Chung-Yu Wang,
Hsin-Yi Wu,
Shu-Yi Ho,
Pin-Rong Chen,
Cheng-Hsun Chuang,
Pei-Jung Hsieh,
Yi-Shin Wu,
Wen-Liang Chen,
Meng-Ju Li,
Yu-chun Wu,
Xin-Yi Huang,
Fung Ling Ng,
Waradee Buddhakosai,
Pei-Chun Huang,
Kuan-Chun Lan,
Chia-Yen Huang,
Shun-Long Weng,
Yeong-Nan Cheng,
Chao Liang,
Wen-Lian Hsu,
Hsien-Da Huang:
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. D296-D302 Pietro Boccaletto,
Magdalena A. Machnicka,
Elzbieta Purta,
Pawel Piatkowski,
Blazej Baginski,
Tomasz Wirecki,
Valérie de Crécy-Lagard,
Robert Ross,
Patrick A. Limbach,
Annika Kotter,
Mark Helm,
Janusz M. Bujnicki:
MODOMICS: a database of RNA modification pathways. 2017 update. D303-D307 Shuangsang Fang,
Lili Zhang,
Jincheng Guo,
Yiwei Niu,
Yang Wu,
Hui Li,
Lianhe Zhao,
Xiyuan Li,
XueYi Teng,
XianHui Sun,
Liang Sun,
Michael Q. Zhang,
Runsheng Chen,
Yi Zhao:
NONCODEV5: a comprehensive annotation database for long non-coding RNAs. D308-D314 Miguel C. Teixeira,
Pedro T. Monteiro,
Margarida Palma,
Catarina Costa,
Cláudia P. Godinho,
Pedro Pais,
Mafalda Cavalheiro,
Miguel Antunes,
Alexandre Lemos,
Tiago Pedreira,
Isabel Sá-Correia:
YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. D348-D353 Francesco Russo,
Sebastiano Di Bella,
Federica Vannini,
Gabriele Berti,
Flavia Scoyni,
Helen Cook,
Alberto Santos,
Giovanni Nigita,
Vincenzo Bonnici,
Alessandro Laganà,
Filippo Geraci,
Alfredo Pulvirenti,
Rosalba Giugno,
Federico De Masi,
Kirstine Belling,
Lars Juhl Jensen,
Søren Brunak,
Marco Pellegrini,
Alfredo Ferro:
miRandola 2017: a curated knowledge base of non-invasive biomarkers. D354-D359 Heonjong Han,
Jae-Won Cho,
Sang-Young Lee,
Ayoung Yun,
Hyojin Kim,
Dasom Bae,
Sunmo Yang,
Chan Yeong Kim,
Muyoung Lee,
Eunbeen Kim,
Sungho Lee,
Byunghee Kang,
Dabin Jeong,
Yaeji Kim,
Hyeon-Nae Jeon,
Haein Jung,
Sunhwee Nam,
Michael Chung,
Jong-Hoon Kim,
Insuk Lee:
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. D380-D386
Protein sequence and structure, motifs, and domains
Mikhail Shugay,
Dmitriy V. Bagaev,
Ivan V. Zvyagin,
Renske M. A. Vroomans,
Jeremy Chase Crawford,
Garry Dolton,
Ekaterina Komech,
Anastasiya L. Sycheva,
Anna E. Koneva,
Evgeniy S. Egorov,
Alexey V. Eliseev,
Ewald van Dyk,
Pradyot Dash,
Meriem Attaf,
Cristina Rius,
Kristin Ladell,
James E. McLaren,
Katherine K. Matthews,
E. Bridie Clemens,
Daniel C. Douek,
Fabio Luciani,
Debbie van Baarle,
Katherine Kedzierska,
Can Kesmir,
Paul G. Thomas,
David A. Price,
Andrew K. Sewell,
Dmitry M. Chudakov:
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. D419-D427 Marc Gouw,
Sushama Michael,
Hugo Sámano-Sánchez,
Manjeet Kumar,
András Zeke,
Benjamin Lang,
Benoit Bely,
Lucía B. Chemes,
Norman E. Davey,
Ziqi Deng,
Francesca Diella,
Clara-Marie Gürth,
Ann-Kathrin Huber,
Stefan Kleinsorg,
Lara S. Schlegel,
Nicolas Palopoli,
Kim Van Roey,
Brigitte Altenberg,
Attila Reményi,
Holger Dinkel,
Toby J. Gibson:
The eukaryotic linear motif resource - 2018 update. D428-D434 Damiano Piovesan,
Francesco Tabaro,
Lisanna Paladin,
Marco Necci,
Ivan Micetic,
Carlo Camilloni,
Norman E. Davey,
Zsuzsanna Dosztányi,
Bálint Mészáros,
Alexander Miguel Monzon,
Gustavo D. Parisi,
Eva Schad,
Pietro Sormanni,
Peter Tompa,
Michele Vendruscolo,
Wim F. Vranken,
Silvio C. E. Tosatto:
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins. D471-D476 Adrian M. Altenhoff,
Natasha Glover,
Clément-Marie Train,
Klara Kaleb,
Alex Warwick Vesztrocy,
David Dylus,
Tarcisio M. Farias,
Karina Zile,
Charles Stevenson,
Jiao Long,
Henning Redestig,
Gaston H. Gonnet,
Christophe Dessimoz:
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. D477-D485 Saqib Mir,
Younes Alhroub,
Stephen Anyango,
David R. Armstrong,
John M. Berrisford,
Alice R. Clark,
Matthew J. Conroy,
Jose M. Dana,
Mandar S. Deshpande,
Deepti Gupta,
Aleksandras Gutmanas,
Pauline Haslam,
Lora Mak,
Abhik Mukhopadhyay,
Nurul Nadzirin,
Typhaine Paysan-Lafosse,
David Sehnal,
Sanchayita Sen,
Oliver S. Smart,
Mihaly Varadi,
Gerard J. Kleywegt,
Sameer Velankar:
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. D486-D492
Metabolic and signalling pathways, enzymes
Amar Koleti,
Raymond Terryn,
Vasileios Stathias,
Caty Chung,
Daniel J. Cooper,
John Paul Turner,
Dusica Vidovic,
Michele Forlin,
Tanya T. Kelley,
Alessandro D'Urso,
Bryce K. Allen,
Denis Torre,
Kathleen M. Jagodnik,
Lily Wang,
Sherry L. Jenkins,
Christopher Mader,
Wen Niu,
Mehdi Fazel,
Naim Mahi,
Marcin Pilarczyk,
Nicholas Clark,
Behrouz Shamsaei,
Jarek Meller,
Juozas Vasiliauskas,
John Reichard,
Mario Medvedovic,
Avi Ma'ayan,
Ajay Pillai,
Stephan C. Schürer:
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. D558-D566 Sunjae Lee,
Cheng Zhang,
Muhammad Arif,
Zhengtao Liu,
Rui Benfeitas,
Gholamreza Bidkhori,
Sumit Deshmukh,
Mohamed Al Shobky,
Alen Lovric,
Jan Boren,
Jens Nielsen,
Mathias Uhlen,
Adil Mardinoglu:
TCSBN: a database of tissue and cancer specific biological networks. D595-D600 David S. Wishart,
Yannick Djoumbou Feunang,
Ana Marcu,
An Chi Guo,
Kevin Liang,
Rosa Vázquez-Fresno,
Tanvir Sajed,
Daniel Johnson,
Carin Li,
Naama Karu,
Zinat Sayeeda,
Elvis J. Lo,
Nazanin Assempour,
Mark V. Berjanskii,
Sandeep Singhal,
David Arndt,
Yongjie Liang,
Hasan Badran,
Jason R. Grant,
Arnau Serra-Cayuela,
Yifeng Liu,
Rupa Mandal,
Vanessa Neveu,
Allison Pon,
Craig Knox,
Michael Wilson,
Claudine Manach,
Augustin Scalbert:
HMDB 4.0: the human metabolome database for 2018. D608-D617 Ron Caspi,
Richard Billington,
Carol A. Fulcher,
Ingrid M. Keseler,
Anamika Kothari,
Markus Krummenacker,
Mario Latendresse,
Peter E. Midford,
Quang Ong,
Wai Kit Ong,
Suzanne M. Paley,
Pallavi Subhraveti,
Peter D. Karp:
The MetaCyc database of metabolic pathways and enzymes. D633-D639 Luís Franco-Serrano,
Sergio Hernández,
Alejandra Calvo,
María A. Severi,
Gabriela Ferragut,
JosepAntoni Perez-Pons,
Jaume Piñol,
Òscar Pich,
Angel Mozo-Villarias,
Isaac Amela,
Enrique Querol,
Juan Cedano:
MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins. D645-D648 Antonio Fabregat,
Steven Jupe,
Lisa Matthews,
Konstantinos Sidiropoulos,
Marc Gillespie,
Phani Garapati,
Robin Haw,
Bijay Jassal,
Florian Korninger,
Bruce May,
Marija Milacic,
Corina Duenas,
Karen Rothfels,
Cristoffer Sevilla,
Veronica Shamovsky,
Solomon Shorser,
Thawfeek M. Varusai,
Guilherme Viteri,
Joel Weiser,
Guanming Wu,
Lincoln Stein,
Henning Hermjakob,
Peter D'Eustachio:
The Reactome Pathway Knowledgebase. D649-D655 Denise Slenter,
Martina Kutmon,
Kristina Hanspers,
Anders Riutta,
Jacob Windsor,
Nuno Nunes,
Jonathan Mélius,
Elisa Cirillo,
Susan L. Coort,
Daniela Digles,
Friederike Ehrhart,
Pieter Giesbertz,
Marianthi Kalafati,
Marvin Martens,
Ryan Miller,
Kozo Nishida,
Linda Rieswijk,
Andra Waagmeester,
Lars M. T. Eijssen,
Chris T. A. Evelo,
Alexander R. Pico,
Egon L. Willighagen:
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. D661-D667
Viruses, bacteria, protozoa and fungi
Francislon S. Oliveira,
John Brestelli,
Shon Cade,
Jie Zheng,
John Iodice,
Steve Fischer,
Cristina Aurrecoechea,
Jessica C. Kissinger,
Brian P. Brunk,
Christian J. Stoeckert Jr.,
Gabriel R. Fernandes,
David S. Roos,
Daniel P. Beiting:
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments. D684-D691
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Daniel J. Rigden, Xosé M. Fernández-Suárez: