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BIOINFORMATICS: betAS: intuitive analysis and visualization of differential alternative splicing using beta distributions

Mariana Ascensão-Ferreira,
Rita Martins-Silva,
Nuno Saraiva-Agostinho,
and Nuno L. Barbosa-Morais

RNA April 2024 30: 337-353; Published in Advance January 26, 2024, doi:10.1261/rna.079764.123

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BIOINFORMATICS: AptaDB: a comprehensive database integrating aptamer–target interactions

Long Chen,
Zhuohang Yu,
Zengrui Wu,
Moran Zhou,
Yimeng Wang,
Xinxin Yu,
Weihua Li,
Guixia Liu,
and Yun Tang

RNA March 2024 30: 189-199; Published in Advance December 19, 2023, doi:10.1261/rna.079784.123

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BIOINFORMATICS: 3D feasibility of 2D RNA–RNA interaction paths by stepwise folding simulations

Irene K. Beckmann,
Maria Waldl,
Sebastian Will,
and Ivo L. Hofacker

RNA February 2024 30: 113-123; Published in Advance December 1, 2023, doi:10.1261/rna.079756.123

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BIOINFORMATICS: Motifs in SARS-CoV-2 evolution

Christopher Barrett,
Andrei C. Bura,
Qijun He,
Fenix W. Huang,
Thomas J.X. Li,
and Christian M. Reidys

RNA January 2024 30: 1-15; Published in Advance October 30, 2023, doi:10.1261/rna.079557.122

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BIOINFORMATICS: VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets

Emna Achouri,
Sébastien A. Felt,
Matthew Hackbart,
Nicole S. Rivera-Espinal,
and Carolina B. López

RNA January 2024 30: 16-25; Published in Advance October 27, 2023, doi:10.1261/rna.079747.123

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BIOINFORMATICS: Discovering pathways through ribozyme fitness landscapes using information theoretic quantification of epistasis

Nathaniel Charest,
Yuning Shen,
Yei-Chen Lai,
Irene A. Chen,
and Joan-Emma Shea

RNA November 2023 29: 1644-1657; Published in Advance August 14, 2023, doi:10.1261/rna.079541.122

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BIOINFORMATICS: Nanoblot: an R-package for visualization of RNA isoforms from long-read RNA-sequencing data

Samuel DeMario,
Kevin Xu,
Kevin He,
and Guillaume F. Chanfreau

RNA August 2023 29: 1099-1107; Published in Advance May 3, 2023, doi:10.1261/rna.079505.122

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BIOINFORMATICS: bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling

Isaac W. Vock and
Matthew D. Simon

RNA July 2023 29: 958-976; Published in Advance April 7, 2023, doi:10.1261/rna.079451.122

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BIOINFORMATICS: clipplotr—a comparative visualization and analysis tool for CLIP data

Anob M. Chakrabarti,
Charlotte Capitanchik,
Jernej Ule,
and Nicholas M. Luscombe

RNA June 2023 29: 715-723; Published in Advance March 9, 2023, doi:10.1261/rna.079326.122

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BIOINFORMATICS: bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures

Brittany Lasher and
David A. Hendrix

RNA May 2023 29: 584-595; Published in Advance February 9, 2023, doi:10.1261/rna.079211.122

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