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SLAYER: a computational framework for identifying synthetic lethal interactions through integrated analysis of cancer dependencies
Ziv Cohen and others
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf052, https://doi.org/10.1093/nargab/lqaf052
Synthetic lethality represents a promising therapeutic approach in precision oncology, yet systematic identification of clinically relevant synthetic lethal interactions remains challenging. Here, we present SLAYER (Synthetic Lethality AnalYsis for Enhanced taRgeted therapy), a computational ...
Identifying similar populations across independent single cell studies without data integration
Oscar González-Velasco and others
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf042, https://doi.org/10.1093/nargab/lqaf042
Supervised and unsupervised methods have emerged to address the complexity of single cell data analysis in the context of large pools of independent studies. Here, we present ClusterFoldSimilarity (CFS), a novel statistical method design to quantify the similarity between cell groups across any ...
Exploring the latent space of transcriptomic data with topic modeling
Filippo Valle and others
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf049, https://doi.org/10.1093/nargab/lqaf049
The availability of high-dimensional transcriptomic datasets is increasing at a tremendous pace, together with the need for suitable computational tools. Clustering and dimensionality reduction methods are popular go-to methods to identify basic structures in these datasets. At the same time, ...
Detection of protein structural hotspots using AI distillation and explainability: application to the DAX-1 protein
Noé Dumas and others
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf047, https://doi.org/10.1093/nargab/lqaf047
AlphaMissense is a valuable resource for discerning important functional regions within proteins, providing pathogenicity heatmaps that highlight the pathogenic risk of specific mutations along the protein sequence. However, due to protein folding and long-range interactions, the actual structural ...
TetRex: a novel algorithm for index-accelerated search of highly conserved motifs
Remy M Schwab and others
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf039, https://doi.org/10.1093/nargab/lqaf039
The scale of modern datasets has necessitated innovations to solve even the most traditional and fundamental of computational problems. Set membership and set cardinality are both examples of simple queries that, for large enough datasets, quickly become challenging using traditional approaches. ...

Editor's Choice Articles

TetRex: a novel algorithm for index-accelerated search of highly conserved motifs
Remy M Schwab and others
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf039, https://doi.org/10.1093/nargab/lqaf039
The scale of modern datasets has necessitated innovations to solve even the most traditional and fundamental of computational problems. Set membership and set cardinality are both examples of simple queries that, for large enough datasets, quickly become challenging using traditional approaches. ...
Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen
Anouk C van Westerhoven and others
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf034, https://doi.org/10.1093/nargab/lqaf034
Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when these chromosomes are missing in the reference genome. ...
IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling
Pierre Hardouin and others
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqaf028, https://doi.org/10.1093/nargab/lqaf028
In addition to their sequence, multiple functions of RNAs are encoded within their structure, which is often difficult to solve using physico-chemical methods. Incorporating low-resolution experimental data such as chemical probing into computational prediction significantly enhances RNA structure ...
Enhancing the annotation of small ORF-altering variants using MORFEE: introducing MORFEEdb, a comprehensive catalog of SNVs affecting upstream ORFs in human 5′UTRs
Caroline Meguerditchian and others
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqaf017, https://doi.org/10.1093/nargab/lqaf017
Non-canonical small open reading frames (sORFs) are among the main regulators of gene expression. The most studied of these are upstream ORFs (upORFs) located in the 5′-untranslated region (UTR) of coding genes. Internal ORFs (intORFs) in the coding sequence and downstream ORFs (dORFs) in the 3′UTR ...
Crafted experiments to evaluate feature selection methods for single-cell RNA-seq data
Siyao Liu and others
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqaf023, https://doi.org/10.1093/nargab/lqaf023
While numerous methods have been developed for analyzing scRNA-seq data, benchmarking various methods remains challenging. There is a lack of ground truth datasets for evaluating novel gene selection and/or clustering methods. We propose the use of crafted experiments , a new approach based upon ...
Impact Factor
4.0
5 year Impact Factor
4.2
CiteScore
8.0
Genetics & Heredity
33 out of 189
Mathematical & Computational Biology
13 out of 67

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