Genomics

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

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

First chromosome-level genome assembly of the colonial tunicate Botryllus schlosseri

1. Olivier De Thier
2. Mohammed M.Tawfeeq
3. Roland Faure
4. Marie Lebel
5. Philippe Dru
6. Simon Blanchoud
7. Alexandre Alié
8. Federico D. Brown
9. Jean-François Flot
10. Stefano Tiozzo

Reviewed by GigaScience

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

1. Larissa S. Arantes
2. Tom Brown
3. Diego De Panis
4. Scott D. Whiting
5. Erin L. LaCasella
6. Gabriella A. Carvajal
7. Adam Kennedy
8. Deana Edmunds
9. Blair P. Bentley
10. Jennifer Balacco
11. Conor Whelan
12. Nivesh Jain
13. Tatiana Tilley
14. Brian O’Toole
15. Patrick Traore
16. Erich D. Jarvis
17. Oliver Berry
18. Peter H. Dutton
19. Lisa M. Komoroske
20. Camila J. Mazzoni

Reviewed by GigaScience

CNSistent integration and feature extraction from somatic copy number profiles

1. Adam Streck
2. Roland F. Schwarz

Reviewed by GigaScience