Literature DB >> 33396976

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

Daniel J Rigden1, Xosé M Fernández2.   

Abstract

The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2021        PMID: 33396976      PMCID: PMC7778882          DOI: 10.1093/nar/gkaa1216

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  89 in total

1.  The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets.

Authors:  Damian Szklarczyk; Annika L Gable; Katerina C Nastou; David Lyon; Rebecca Kirsch; Sampo Pyysalo; Nadezhda T Doncheva; Marc Legeay; Tao Fang; Peer Bork; Lars J Jensen; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

2.  KinaseMD: kinase mutations and drug response database.

Authors:  Ruifeng Hu; Haodong Xu; Peilin Jia; Zhongming Zhao
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

3.  PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins.

Authors:  Tamas Lazar; Elizabeth Martínez-Pérez; Federica Quaglia; András Hatos; Lucía B Chemes; Javier A Iserte; Nicolás A Méndez; Nicolás A Garrone; Tadeo E Saldaño; Julia Marchetti; Ana Julia Velez Rueda; Pau Bernadó; Martin Blackledge; Tiago N Cordeiro; Eric Fagerberg; Julie D Forman-Kay; Maria S Fornasari; Toby J Gibson; Gregory-Neal W Gomes; Claudiu C Gradinaru; Teresa Head-Gordon; Malene Ringkjøbing Jensen; Edward A Lemke; Sonia Longhi; Cristina Marino-Buslje; Giovanni Minervini; Tanja Mittag; Alexander Miguel Monzon; Rohit V Pappu; Gustavo Parisi; Sylvie Ricard-Blum; Kiersten M Ruff; Edoardo Salladini; Marie Skepö; Dmitri Svergun; Sylvain D Vallet; Mihaly Varadi; Peter Tompa; Silvio C E Tosatto; Damiano Piovesan
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

4.  ViruSurf: an integrated database to investigate viral sequences.

Authors:  Arif Canakoglu; Pietro Pinoli; Anna Bernasconi; Tommaso Alfonsi; Damianos P Melidis; Stefano Ceri
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

5.  MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations.

Authors:  Sneha Rath; Rohit Sharma; Rahul Gupta; Tslil Ast; Connie Chan; Timothy J Durham; Russell P Goodman; Zenon Grabarek; Mary E Haas; Wendy H W Hung; Pallavi R Joshi; Alexis A Jourdain; Sharon H Kim; Anna V Kotrys; Stephanie S Lam; Jason G McCoy; Joshua D Meisel; Maria Miranda; Apekshya Panda; Anupam Patgiri; Robert Rogers; Shayan Sadre; Hardik Shah; Owen S Skinner; Tsz-Leung To; Melissa A Walker; Hong Wang; Patrick S Ward; Jordan Wengrod; Chen-Ching Yuan; Sarah E Calvo; Vamsi K Mootha
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

6.  PROTAC-DB: an online database of PROTACs.

Authors:  Gaoqi Weng; Chao Shen; Dongsheng Cao; Junbo Gao; Xiaowu Dong; Qiaojun He; Bo Yang; Dan Li; Jian Wu; Tingjun Hou
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

7.  CSVS, a crowdsourcing database of the Spanish population genetic variability.

Authors:  María Peña-Chilet; Gema Roldán; Javier Perez-Florido; Francisco M Ortuño; Rosario Carmona; Virginia Aquino; Daniel Lopez-Lopez; Carlos Loucera; Jose L Fernandez-Rueda; Asunción Gallego; Francisco García-Garcia; Anna González-Neira; Guillermo Pita; Rocío Núñez-Torres; Javier Santoyo-López; Carmen Ayuso; Pablo Minguez; Almudena Avila-Fernandez; Marta Corton; Miguel Ángel Moreno-Pelayo; Matías Morin; Alvaro Gallego-Martinez; Jose A Lopez-Escamez; Salud Borrego; Guillermo Antiñolo; Jorge Amigo; Josefa Salgado-Garrido; Sara Pasalodos-Sanchez; Beatriz Morte; Ángel Carracedo; Ángel Alonso; Joaquín Dopazo
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

8.  From ArrayExpress to BioStudies.

Authors:  Ugis Sarkans; Anja Füllgrabe; Ahmed Ali; Awais Athar; Ehsan Behrangi; Nestor Diaz; Silvie Fexova; Nancy George; Haider Iqbal; Sandeep Kurri; Jhoan Munoz; Juan Rada; Irene Papatheodorou; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

9.  FlyBase: updates to the Drosophila melanogaster knowledge base.

Authors:  Aoife Larkin; Steven J Marygold; Giulia Antonazzo; Helen Attrill; Gilberto Dos Santos; Phani V Garapati; Joshua L Goodman; L Sian Gramates; Gillian Millburn; Victor B Strelets; Christopher J Tabone; Jim Thurmond
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

10.  Genome Variation Map: a worldwide collection of genome variations across multiple species.

Authors:  Cuiping Li; Dongmei Tian; Bixia Tang; Xiaonan Liu; Xufei Teng; Wenming Zhao; Zhang Zhang; Shuhui Song
Journal:  Nucleic Acids Res       Date:  2020-11-10       Impact factor: 16.971

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  11 in total

1.  Omics Analyses: How to Navigate Through a Constant Data Deluge.

Authors:  Thomas Denecker; Gaëlle Lelandais
Journal:  Methods Mol Biol       Date:  2022

Review 2.  Current status of PTMs structural databases: applications, limitations and prospects.

Authors:  Alexandre G de Brevern; Joseph Rebehmed
Journal:  Amino Acids       Date:  2022-01-12       Impact factor: 3.520

3.  Building Structural Models of a Whole Mycoplasma Cell.

Authors:  Martina Maritan; Ludovic Autin; Jonathan Karr; Markus W Covert; Arthur J Olson; David S Goodsell
Journal:  J Mol Biol       Date:  2021-11-10       Impact factor: 5.469

Review 4.  Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes.

Authors:  Jacopo Umberto Verga; Matthew Huff; Diarmuid Owens; Bethany J Wolf; Gary Hardiman
Journal:  Int J Environ Res Public Health       Date:  2022-01-05       Impact factor: 3.390

Review 5.  Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions.

Authors:  Andrés Rincón-Riveros; Duvan Morales; Josefa Antonia Rodríguez; Victoria E Villegas; Liliana López-Kleine
Journal:  Int J Mol Sci       Date:  2021-10-22       Impact factor: 5.923

Review 6.  DBHR: a collection of databases relevant to human research.

Authors:  Shahid Ullah; Wajeeha Rahman; Farhan Ullah; Gulzar Ahmad; Muhmmad Ijaz; Tianshun Gao
Journal:  Future Sci OA       Date:  2021-01-20

7.  Survey of bioinformatics courses and concentrations in ALA-accredited master's programs.

Authors:  Leah Graham; Melissa Moleirinho
Journal:  J Can Health Libr Assoc       Date:  2022-08-04

Review 8.  Metagenomics: a path to understanding the gut microbiome.

Authors:  Sandi Yen; Jethro S Johnson
Journal:  Mamm Genome       Date:  2021-07-14       Impact factor: 2.957

Review 9.  Molecular Biology in Treatment Decision Processes-Neuro-Oncology Edition.

Authors:  Andra V Krauze; Kevin Camphausen
Journal:  Int J Mol Sci       Date:  2021-12-10       Impact factor: 5.923

Review 10.  An innovative user-friendly platform for Covid-19 pandemic databases and resources.

Authors:  Shahid Ullah; Anees Ullah; Wajeeha Rahman; Farhan Ullah; Sher Bahadar Khan; Gulzar Ahmad; Muhammad Ijaz; Tianshun Gao
Journal:  Comput Methods Programs Biomed Update       Date:  2021-09-26
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