Genomics

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

Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression

1. Jie Lin
2. Yujian Wen
3. Ji Tang
4. Xuecong Zhang
5. Huanlin Zhang
6. Hao Zhu

• Curated by eLife

  eLife Assessment

  This valuable study uses tools of population and functional genomics to examine long non-coding RNAs (lncRNAs) in the context of human evolution. Analyses of computationally predicted human-specific lncRNAs and their genomic targets lead to the development of hypotheses regarding the potential roles of these genetic elements in human biology. The conclusions regarding evolutionary acceleration and adaptation, however, only incompletely take data and literature on human/chimpanzee genetics and functional genomics into account.

Reviewed by eLife

CellCover Defines Marker Gene Panels Capturing Developmental Progression in Neocortical Neural Stem Cell Identity

1. Lanlan Ji
2. An Wang
3. Shreyash Sonthalia
4. Seungmae Seo
5. Daniel Q Naiman
6. Laurent Younes
7. Carlo Colantuoni
8. Donald Geman

• Curated by eLife

  eLife Assessment

  This study offers a valuable methodological advance by introducing a gene panel selection approach that captures combinatorial specificity to define cell identity. The findings address key limitations of current single-gene marker methods. The evidence is compelling, but would be strengthened by further validation of rare cell states and unexpected marker categories.

Reviewed by eLife

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