Literature DB >> 21940779

RNAcentral: A vision for an international database of RNA sequences.

Alex Bateman, Shipra Agrawal, Ewan Birney, Elspeth A Bruford, Janusz M Bujnicki, Guy Cochrane, James R Cole, Marcel E Dinger, Anton J Enright, Paul P Gardner, Daniel Gautheret, Sam Griffiths-Jones, Jen Harrow, Javier Herrero, Ian H Holmes, Hsien-Da Huang, Krystyna A Kelly, Paul Kersey, Ana Kozomara, Todd M Lowe, Manja Marz, Simon Moxon, Kim D Pruitt, Tore Samuelsson, Peter F Stadler, Albert J Vilella, Jan-Hinnerk Vogel, Kelly P Williams, Mathew W Wright, Christian Zwieb.   

Abstract

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.

Entities:  

Mesh:

Substances:

Year:  2011        PMID: 21940779      PMCID: PMC3198587          DOI: 10.1261/rna.2750811

Source DB:  PubMed          Journal:  RNA        ISSN: 1355-8382            Impact factor:   4.942


  50 in total

1.  Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA.

Authors:  Catherine L Jopling; Minkyung Yi; Alissa M Lancaster; Stanley M Lemon; Peter Sarnow
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

2.  Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays.

Authors:  Philipp Kapranov; Jorg Drenkow; Jill Cheng; Jeffrey Long; Gregg Helt; Sujit Dike; Thomas R Gingeras
Journal:  Genome Res       Date:  2005-07       Impact factor: 9.043

Review 3.  How ribosomes make peptide bonds.

Authors:  Marina V Rodnina; Malte Beringer; Wolfgang Wintermeyer
Journal:  Trends Biochem Sci       Date:  2006-12-08       Impact factor: 13.807

Review 4.  Antibiotics and the ribosome.

Authors:  Tanel Tenson; Alexander Mankin
Journal:  Mol Microbiol       Date:  2006-03       Impact factor: 3.501

5.  Characterization of the piRNA complex from rat testes.

Authors:  Nelson C Lau; Anita G Seto; Jinkuk Kim; Satomi Kuramochi-Miyagawa; Toru Nakano; David P Bartel; Robert E Kingston
Journal:  Science       Date:  2006-06-15       Impact factor: 47.728

6.  Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance.

Authors:  Ramanjulu Sunkar; Avnish Kapoor; Jian-Kang Zhu
Journal:  Plant Cell       Date:  2006-07-21       Impact factor: 11.277

7.  The tmRDB and SRPDB resources.

Authors:  Ebbe Sloth Andersen; Magnus Alm Rosenblad; Niels Larsen; Jesper Cairo Westergaard; Jody Burks; Iwona K Wower; Jacek Wower; Jan Gorodkin; Tore Samuelsson; Christian Zwieb
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

8.  Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.

Authors:  Norihiro Maeda; Takeya Kasukawa; Rieko Oyama; Julian Gough; Martin Frith; Pär G Engström; Boris Lenhard; Rajith N Aturaliya; Serge Batalov; Kirk W Beisel; Carol J Bult; Colin F Fletcher; Alistair R R Forrest; Masaaki Furuno; David Hill; Masayoshi Itoh; Mutsumi Kanamori-Katayama; Shintaro Katayama; Masaru Katoh; Tsugumi Kawashima; John Quackenbush; Timothy Ravasi; Brian Z Ring; Kazuhiro Shibata; Koji Sugiura; Yoichi Takenaka; Rohan D Teasdale; Christine A Wells; Yunxia Zhu; Chikatoshi Kai; Jun Kawai; David A Hume; Piero Carninci; Yoshihide Hayashizaki
Journal:  PLoS Genet       Date:  2006-04       Impact factor: 5.917

9.  RNAdb 2.0--an expanded database of mammalian non-coding RNAs.

Authors:  Ken C Pang; Stuart Stephen; Marcel E Dinger; Pär G Engström; Boris Lenhard; John S Mattick
Journal:  Nucleic Acids Res       Date:  2006-12-01       Impact factor: 16.971

10.  The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.

Authors:  Ibtissem Grissa; Gilles Vergnaud; Christine Pourcel
Journal:  BMC Bioinformatics       Date:  2007-05-23       Impact factor: 3.169

View more
  36 in total

1.  A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

Authors:  Elena Rivas; Raymond Lang; Sean R Eddy
Journal:  RNA       Date:  2011-12-22       Impact factor: 4.942

Review 2.  Computational Methods and Online Resources for Identification of piRNA-Related Molecules.

Authors:  Yajun Liu; Aimin Li; Guo Xie; Guangming Liu; Xinhong Hei
Journal:  Interdiscip Sci       Date:  2021-04-22       Impact factor: 2.233

3.  An RNA Mapping DataBase for curating RNA structure mapping experiments.

Authors:  Pablo Cordero; Julius B Lucks; Rhiju Das
Journal:  Bioinformatics       Date:  2012-09-12       Impact factor: 6.937

4.  Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.

Authors:  Lars Barquist; Sarah W Burge; Paul P Gardner
Journal:  Curr Protoc Bioinformatics       Date:  2016-06-20

5.  Content discovery and retrieval services at the European Nucleotide Archive.

Authors:  Nicole Silvester; Blaise Alako; Clara Amid; Ana Cerdeño-Tárraga; Iain Cleland; Richard Gibson; Neil Goodgame; Petra Ten Hoopen; Simon Kay; Rasko Leinonen; Weizhong Li; Xin Liu; Rodrigo Lopez; Nima Pakseresht; Swapna Pallreddy; Sheila Plaister; Rajesh Radhakrishnan; Marc Rossello; Alexander Senf; Dmitriy Smirnov; Ana Luisa Toribio; Daniel Vaughan; Vadim Zalunin; Guy Cochrane
Journal:  Nucleic Acids Res       Date:  2014-11-17       Impact factor: 16.971

Review 6.  Computational analysis of noncoding RNAs.

Authors:  Stefan Washietl; Sebastian Will; David A Hendrix; Loyal A Goff; John L Rinn; Bonnie Berger; Manolis Kellis
Journal:  Wiley Interdiscip Rev RNA       Date:  2012-09-18       Impact factor: 9.957

7.  RNAlien - Unsupervised RNA family model construction.

Authors:  Florian Eggenhofer; Ivo L Hofacker; Christian Höner Zu Siederdissen
Journal:  Nucleic Acids Res       Date:  2016-06-21       Impact factor: 16.971

8.  piRNAs and Their Functions in the Brain.

Authors:  Lingjun Zuo; Zhiren Wang; Yunlong Tan; Xiangning Chen; Xingguang Luo
Journal:  Int J Hum Genet       Date:  2016 Mar-Jun       Impact factor: 0.226

9.  Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base.

Authors:  Alejandro Rodríguez-Iglesias; Alejandro Rodríguez-González; Alistair G Irvine; Ane Sesma; Martin Urban; Kim E Hammond-Kosack; Mark D Wilkinson
Journal:  Front Plant Sci       Date:  2016-05-12       Impact factor: 5.753

Review 10.  Data integration in the era of omics: current and future challenges.

Authors:  David Gomez-Cabrero; Imad Abugessaisa; Dieter Maier; Andrew Teschendorff; Matthias Merkenschlager; Andreas Gisel; Esteban Ballestar; Erik Bongcam-Rudloff; Ana Conesa; Jesper Tegnér
Journal:  BMC Syst Biol       Date:  2014-03-13
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.