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Journal Article

A CRISPR-SpCas9M-reporting system for efficient and rapid genome editing in Caulobacter crescentus

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Jingxian Sun and others
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf353, https://doi.org/10.1093/nar/gkaf353
Published: 29 April 2025
Journal Article

FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins

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Kenji Gerhardt and others
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf348, https://doi.org/10.1093/nar/gkaf348
Published: 26 April 2025
Journal Article

A powerful and highly efficient PAI-mediated transgenesis approach in Drosophila

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Wangfei Shi and others
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf317, https://doi.org/10.1093/nar/gkaf317
Published: 23 April 2025
Journal Article

DirectHRD enables sensitive scar-based classification of homologous recombination deficiency

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Ruolin Liu and others
Nucleic Acids Research, Volume 53, Issue 8, 8 May 2025, gkaf313, https://doi.org/10.1093/nar/gkaf313
Published: 22 April 2025
Journal Article

SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics

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Ren-Gang Zhang and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf320, https://doi.org/10.1093/nar/gkaf320
Published: 18 April 2025
Journal Article

Rapid discovery of functional RNA domains

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Brandon Latifi and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf307, https://doi.org/10.1093/nar/gkaf307
Published: 17 April 2025
Journal Article

NicOPURE: nickless RNA circularization and one-step purification with engineered group II introns and cyclizing UTRs

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Xiang Gao and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf310, https://doi.org/10.1093/nar/gkaf310
Published: 16 April 2025
Journal Article

Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data

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Augustinas Sukys and Ramon Grima
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf295, https://doi.org/10.1093/nar/gkaf295
Published: 16 April 2025
Journal Article

pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data

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J Carlos Angel and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf289, https://doi.org/10.1093/nar/gkaf289
Published: 14 April 2025
Journal Article

LIET model: capturing the kinetics of RNA polymerase from loading to termination

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Jacob T Stanley and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf246, https://doi.org/10.1093/nar/gkaf246
Published: 14 April 2025
Journal Article

Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model

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Qilong Lai and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf305, https://doi.org/10.1093/nar/gkaf305
Published: 14 April 2025
Journal Article

DuplexDiscoverer: a computational method for the analysis of experimental duplex RNA–RNA interaction data

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Egor Semenchenko and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf266, https://doi.org/10.1093/nar/gkaf266
Published: 12 April 2025
Journal Article

Selict-seq profiles genome-wide off-target effects in adenosine base editing

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Kexin Yuan and others
Nucleic Acids Research, Volume 53, Issue 7, 24 April 2025, gkaf281, https://doi.org/10.1093/nar/gkaf281
Published: 10 April 2025
Journal Article

True length of diverse capped RNA sequencing (TLDR-seq): 5′–3′-end sequencing of capped RNAs regardless of 3′-end status

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Jamie Auxillos and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf240, https://doi.org/10.1093/nar/gkaf240
Published: 04 April 2025
Journal Article

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning

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Sowmya Ramaswamy Krishnan and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf239, https://doi.org/10.1093/nar/gkaf239
Published: 02 April 2025
Journal Article

CellPie: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization

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Sokratia Georgaka and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf251, https://doi.org/10.1093/nar/gkaf251
Published: 01 April 2025
Journal Article

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities

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Weiwei Yang and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf226, https://doi.org/10.1093/nar/gkaf226
Published: 29 March 2025
Journal Article

MAIGRET: a CRISPR-based immunoassay that employs antibody-induced cell-free transcription of CRISPR guide RNA strands

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Francesca Miceli and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf238, https://doi.org/10.1093/nar/gkaf238
Published: 28 March 2025
Journal Article

Efficient DNA- and virus-free engineering of cellular transcriptomic states using dCas9 ribonucleoprotein (dRNP) complexes

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Tobias Schmidt and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf235, https://doi.org/10.1093/nar/gkaf235
Published: 28 March 2025
Journal Article

CASCADE-Cas3 enables highly efficient genome engineering in Streptomyces species

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Christopher M Whitford and others
Nucleic Acids Research, Volume 53, Issue 6, 11 April 2025, gkaf214, https://doi.org/10.1093/nar/gkaf214
Published: 26 March 2025