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Plasmids pick a bacterial partner before committing to conjugation

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (17)

Bacterial conjugation was first described by Lederberg and Tatum in the 1940s following the discovery of the F plasmid. During conjugation a plasmid i......

Physical interaction between MSL2 and CLAMP assures direct cooperativity and prevents competition at composite binding sites

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (17)

MSL2, the DNA-binding subunit of the Drosophila dosage compensation complex, cooperates with the ubiquitous protein CLAMP to bind MSL recognition elem......

Photoswitchable molecular glue for RNA: reversible photocontrol of structure and function of the ribozyme

期刊: NUCLEIC ACIDS RESEARCH, 2023; ()

Single-stranded RNA folds into a variety of secondary and higher-order structures. Distributions and dynamics of multiple RNA conformations are respon......

Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles

期刊: NUCLEIC ACIDS RESEARCH, 2023; ()

Pathway analysis, including nontopology-based (non-TB) and topology-based (TB) methods, is widely used to interpret the biological phenomena underlyin......

TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (D1)

AI-driven protein structure prediction, most notably AlphaFold2 (AF2) opens new frontiers for almost all fields of structural biology. As traditional ......

HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (D1)

HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. H......

The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (D1)

The identification of unknown chemicals has emerged as a significant issue in untargeted metabolome analysis owing to the limited availability of puri......

GeneFriends: gene co-expression databases and tools for humans and model organisms

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (D1)

Gene co-expression analysis has emerged as a powerful method to provide insights into gene function and regulation. The rapid growth of publicly avail......

Single-cell gene regulatory network prediction by explainable AI

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (4)

The molecular heterogeneity of cancer cells contributes to the often partial response to targeted therapies and relapse of disease due to the escape o......

Precise homology-directed installation of large genomic edits in human cells with cleaving and nicking high-specificity Cas9 variants

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (7)

Homology-directed recombination (HDR) between donor constructs and acceptor genomic sequences cleaved by programmable nucleases, permits installing la......

The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (10)

The marine thermophilic archaeon Nanoarchaeum equitans possesses a monomeric primase encompassing the conserved domains of the small catalytic and the......

IRSOM2: a web server for predicting bifunctional RNAs

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (W1)

Recent advances have shown that some biologically active non-coding RNAs (ncRNAs) are actually translated into polypeptides that have a physiological ......

DksA is a conserved master regulator of stress response in Acinetobacter baumannii

期刊: NUCLEIC ACIDS RESEARCH, 2023; 51 (12)

Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The gener......

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