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Biochemistry & Molecular Biology
Catherine M. Farrell et al.
Summary: RefSeq Functional Elements (RefSeqFEs) are experimentally validated human and mouse nongenic elements provided by NCBI, offering rich functional details and transparent experimental evidence, with multiple uses for basic functional discovery, bioinformatics studies, and genetic variant interpretation.
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Biochemistry & Molecular Biology
Eric W. Sayers et al.
Summary: GenBank is a comprehensive public database with over 2.5 billion nucleotide sequences totaling 15.3 trillion base pairs for 504,000 formally described species. Recent updates include resources for SARS-CoV-2 virus data, upcoming changes to GI identifiers, and advice for providing contextual metadata in submissions.
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Biochemistry & Molecular Biology
Toshihisa Okido et al.
Summary: The Bioinformation and DDBJ (DNA Data Bank of Japan) Center operates archival databases and provides services for life science researchers, including nucleotide sequences, study information, and other genomic data-related services.
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(2022)
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Biochemistry & Molecular Biology
Carla Cummins et al.
Summary: The European Nucleotide Archive, maintained at EMBL-EBI, offers free services for deposition and access to open nucleotide sequencing data, playing a crucial role in advancing scientific research.
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(2022)
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Biochemistry & Molecular Biology
Jiyao Wang et al.
Summary: iCn3D was initially developed as a web-based 3D molecular viewer and evolved into a full-featured interactive structural analysis software. By sharing URLs, users can share annotated molecular scenes and underlying data. Recently, Python and Node.js are used to systematically analyze large structural datasets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Editorial Material
Microbiology
Patricia A. Bradford et al.
Summary: The inconsistent assignment of names to beta-lactamase variants has caused confusion in published literature. The widespread use of whole genome sequencing has led to a rapid increase in the number of new beta-lactamase genes. In November 2021, an international group of beta-lactamase experts met virtually to establish a consensus on the naming of naturally-occurring beta-lactamase genes. This document formalizes the process for naming novel beta-lactamases and their subsequent publication.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Biochemistry & Molecular Biology
Sunghwan Kim et al.
Summary: PubChem is a public chemical database that serves as a vital resource for biomedical research communities. It provides information on chemicals related to biological targets, helping users analyze and interpret the biological activity data of molecules. The database contains data from hundreds of contributors and is organized into various collections based on different record types.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
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Multidisciplinary Sciences
Joannella Morales et al.
Summary: Comprehensive genome annotation is crucial for understanding clinically relevant variants, but the lack of standardized reporting and browser display complicates interpretation and reporting. To address this, Ensembl/GENCODE and RefSeq launched the MATCHED Annotation from NCBI and EMBL-EBI (MANE) collaboration to define universal standards for variant reporting and browser display. The MANE transcript sets provide representative transcripts for each human protein-coding gene, improving consistency and facilitating clinical interpretation.
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Multidisciplinary Sciences
Sergey Nurk et al.
Summary: The Telomere-to-Telomere (T2T) Consortium has presented a complete sequence of a human genome, T2T-CHM13, which covers the whole genome except for the Y chromosome. This new sequence includes gapless assemblies, error corrections in previous references, and nearly 200 million base pairs of additional sequence with gene predictions, including protein coding genes. The completion of important regions allows for further studies on genetic variations and functions.
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Biochemistry & Molecular Biology
Eric W. Sayers et al.
Summary: The National Center for Biotechnology Information (NCBI) offers a wide range of online resources for biological information and data, including GenBank (R) nucleic acid sequence database and PubMed (R) database of citations and abstracts. Entrez system allows search and retrieval operations for most of these data, with E-utilities serving as the programming interface. Additional resources such as PMC, Bookshelf, Genome Data Viewer, SRA, ClinVar, dbSNP, dbVar, Pathogen Detection, BLAST, Primer-BLAST, IgBLAST, iCn3D, and PubChem are also accessible through the NCBI home page.
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(2021)
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Multidisciplinary Sciences
Brad Brown et al.
Summary: The study presents an analysis of the GenomeTrakr WGS Network's impact on food safety, showing that adding WGS isolates to the NCBI database is associated with reducing illnesses from WGS pathogens. According to cost benefit analysis, the program likely broke even in its second year of implementation and could produce increasing public health benefits as the network matures.
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Multidisciplinary Sciences
John Jumper et al.
Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.
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Multidisciplinary Sciences
An-Ni Zhang et al.
Summary: Antibiotic resistance genes are common among bacteria, but not all pose high risks to human health. Researchers have developed an omics-based framework to rank these genes by risk, taking into account their enrichment in human associated environments, gene mobility, and host pathogenicity.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Michael Feldgarden et al.
Summary: With the advancement of technology, in silico approaches to assessing AMR gene content have become possible. NCBI has developed a comprehensive AMR gene database and AMR gene detection tool, expanding the Reference Gene Catalog and releasing AMRFinderPlus to provide a more accurate means of identifying AMR genes and determining their relationship with phenotypes.
SCIENTIFIC REPORTS
(2021)
Article
Virology
Aine O'Toole et al.
Summary: The global virus genomics community has responded unprecedentedly to the SARS-CoV-2 pandemic, leading to significant advances in 'real-time' generation and sharing of genomic data. The development of new analytical methods, such as pangolin, has been necessary to handle the rapid growth in virus genome data production. Pangolin has processed nearly two million virus genomes, aiding in SARS-CoV-2 genomic epidemiology and providing researchers with valuable information about the pandemic's transmission lineages.
Article
Biochemistry & Molecular Biology
Masanori Arita et al.
Summary: The International Nucleotide Sequence Database Collaboration (INSDC) has been a core infrastructure for collecting and providing nucleotide sequence data and metadata for over 30 years. Collaboratively maintained by three partner organizations, INSDC benefits science and communities worldwide.
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(2021)
Article
Biochemistry & Molecular Biology
Sunghwan Kim et al.
Summary: PubChem, a popular chemical information resource, has made substantial improvements in the past two years by adding data from over 100 new sources, updating its homepage and record pages, introducing new services like the Periodic Table and Pathway pages, and creating a special data collection related to COVID-19 and SARS-CoV-2 in response to the pandemic.
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Biochemistry & Molecular Biology
Eric W. Sayers et al.
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Biochemistry & Molecular Biology
Shennan Lu et al.
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Melissa J. Landrum et al.
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Richa Agarwala et al.
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Review
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Sunghwan Kim
EXPERT OPINION ON DRUG DISCOVERY
(2016)
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Wendy S. Rubinstein et al.
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Jian Ye et al.
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