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Section: Database Issue
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Journal Article

ChiTaRS 8.0: the comprehensive database of chimeric transcripts and RNA-seq data with applications in liquid biopsy

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Dylan DSouza and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1302–D1312, https://doi.org/10.1093/nar/gkae1126
Published: 16 December 2024
Journal Article

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

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Mitja M Zdouc and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D678–D690, https://doi.org/10.1093/nar/gkae1115
Published: 09 December 2024
Journal Article

Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery

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Annalisa Buniello and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1467–D1475, https://doi.org/10.1093/nar/gkae1128
Published: 06 December 2024
Journal Article

The RodentGPOmics Atlas: a comprehensive database of rodent biology for genomes and pathogens

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Zhiwen Jiang and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1144–D1150, https://doi.org/10.1093/nar/gkae1074
Published: 06 December 2024
Journal Article

Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools

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Frederic B Bastian and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D878–D885, https://doi.org/10.1093/nar/gkae1118
Published: 05 December 2024
Journal Article

Ensembl 2025

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Sarah C Dyer and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D948–D957, https://doi.org/10.1093/nar/gkae1071
Published: 04 December 2024
Journal Article

MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models

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Alexander W Clarke and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D116–D128, https://doi.org/10.1093/nar/gkae1094
Published: 30 November 2024
Journal Article

Immunosenescence Inventory—a multi-omics database for immune aging research

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Hao Li and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1047–D1054, https://doi.org/10.1093/nar/gkae1102
Published: 30 November 2024
Journal Article

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

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Stephen K Burley and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D564–D574, https://doi.org/10.1093/nar/gkae1091
Published: 28 November 2024
Journal Article

EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2024

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Matthew Thakur and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D10–D19, https://doi.org/10.1093/nar/gkae1089
Published: 28 November 2024
Journal Article

CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data

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CZI Cell Science Program and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D886–D900, https://doi.org/10.1093/nar/gkae1142
Published: 28 November 2024
Journal Article

Update of the FANTOM web resource: enhancement for studying noncoding genomes

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Tomoe Nobusada and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D419–D424, https://doi.org/10.1093/nar/gkae1047
Published: 27 November 2024
Journal Article

REDIportal: toward an integrated view of the A-to-I editing

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Pietro D’Addabbo and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D233–D242, https://doi.org/10.1093/nar/gkae1083
Published: 26 November 2024
Journal Article

PHI-base – the multi-species pathogen–host interaction database in 2025

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Martin Urban and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D826–D838, https://doi.org/10.1093/nar/gkae1084
Published: 26 November 2024
Journal Article

The Natural Products Atlas 3.0: extending the database of microbially derived natural products

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Ella F Poynton and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D691–D699, https://doi.org/10.1093/nar/gkae1093
Published: 26 November 2024
Journal Article

COCONUT 2.0: a comprehensive overhaul and curation of the collection of open natural products database

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Venkata Chandrasekhar and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D634–D643, https://doi.org/10.1093/nar/gkae1063
Published: 26 November 2024
Journal Article

ClinVar: updates to support classifications of both germline and somatic variants

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Melissa J Landrum and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1313–D1321, https://doi.org/10.1093/nar/gkae1090
Published: 23 November 2024
Journal Article

miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification

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Jiatong Xu and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D138–D146, https://doi.org/10.1093/nar/gkae1086
Published: 23 November 2024
Journal Article

miRTarBase 2025: updates to the collection of experimentally validated microRNA–target interactions

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Shidong Cui and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D147–D156, https://doi.org/10.1093/nar/gkae1072
Published: 23 November 2024
Journal Article

GoFCards: an integrated database and analytic platform for gain of function variants in humans

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Wenjing Zhao and others
Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D976–D988, https://doi.org/10.1093/nar/gkae1079
Published: 23 November 2024