Genomics

RNA-SeqEZPZ: A Point-and-Click Pipeline for Comprehensive Transcriptomics Analysis with Interactive Visualizations

1. Cenny Taslim
2. Yuan Zhang
3. Genevieve C. Kendall
4. Emily R. Theisen

Reviewed by GigaScience

Neisseria gonorrhoeae LIN codes provide a robust, multi-resolution lineage nomenclature

1. Anastasia Unitt
2. Made A Krisna
3. Kasia M Parfitt
4. Keith A Jolley
5. Martin CJ Maiden
6. Odile B Harrison

• Curated by eLife

  eLife Assessment

  This important study introduces the Life Identification Number (LIN) coding system as a powerful and versatile approach for classifying Neisseria gonorrhoeae lineages. The authors show that LIN codes capture both previously defined lineages and their relationships in a way that aligns with the species' phylogenetic structure. The compelling evidence presented, together with its integration into the PubMLST platform, underscores its strong potential to enhance epidemiological surveillance and advance our understanding of gonococcal population biology.

Reviewed by eLife

Nonlinear transcriptional responses to gradual modulation of transcription factor dosage

1. Júlia Domingo
2. Mariia Minaeva
3. John A Morris
4. Samuel Ghatan
5. Marcello Ziosi
6. Neville E Sanjana
7. Tuuli Lappalainen

• Curated by eLife

  eLife Assessment

  This important work develops a new protocol to experimentally perturb target genes across a quantitative range of expression levels in cell lines. The evidence supporting their new perturbation approach is convincing, and we propose that focusing on single modality (activation or inhibition) would be sufficient to draw their conclusions. The study will be of broad interest to scientists in the fields of functional genomics and biotechnology.

Reviewed by eLife

Crossing host boundaries: the evolutionary drivers and correlates of viral host jumps

1. Cedric C.S. Tan
2. Lucy van Dorp
3. Francois Balloux

Reviewed by Rapid Reviews Infectious Diseases

Conservation of chromatin states and their association with transcription factors in land plants

1. Vikas Shukla
2. Elin Axelsson
3. Tetsuya Hisanaga
4. Jim Haseloff
5. Frédéric Berger
6. Facundo Romani

Reviewed by Review Commons

TinkerHap - A Novel Read-Based Phasing Algorithm with Integrated Multi-Method Support for Enhanced Accuracy

1. Uri Hartmann
2. Eran Shaham
3. Dafna Nathan
4. Ilana Blech
5. Danny Zeevi

Reviewed by GigaScience

The genetic control of rapid genome content divergence in Arabidopsis thaliana

1. Christopher J Fiscus
2. Daniel Koenig

• Curated by eLife

  eLife Assessment

  This important study systematically investigates repeat expansion in the plant Arabidopsis thaliana using a new k-mer-based method, expanding on smaller studies to more comprehensively identify cis- and trans-acting loci associated with repeat dynamics. The approach is methodologically sound and broadly applicable to large-scale short-read datasets for assessing copy number variation and genomic repeat content. While convincing in its scope and novelty, the findings would be further strengthened with exploratory analyses of datasets from other species with more or fewer repeats in their genomes.

Reviewed by eLife

Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases

1. Raehoon Jeong
2. Martha L Bulyk

• Curated by eLife

  eLife Assessment

  This paper addresses a significant question regarding the low overlap between genetic discoveries for human complex diseases and those for gene expression by emphasizing the contribution of cell-type-specific chromatin accessibility QTLs. The analyses supporting the main claims are convincing, and the key conclusions are valuable and of interest to readers in the fields of human genetics and functional genomics.

Reviewed by eLife

PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

1. Engy Nasr
2. Anna Henger
3. Björn Grüning
4. Paul Zierep
5. Bérénice Batut

Reviewed by GigaScience

A high-quality reference genome for the Ural Owl ( Strix uralensis ) enables investigations of cell cultures as a genomic resource for endangered species

1. Ioannis Chrysostomakis
2. Annika Mozer
3. Camilla Bruno Di-Nizo
4. Dominik Fischer
5. Nafiseh Sargheini
6. Laura von der Mark
7. Bruno Huettel
8. Jonas J. Astrin
9. Till Töpfer
10. Astrid Böhne

Reviewed by GigaScience