Genomics

Predicting dynamic expression patterns in budding yeast with a fungal DNA language model

1. Kuan-Hao Chao
2. Majed Mohamed Magzoub
3. Emily Stoops
4. Sean Hackett
5. Johannes Linder
6. David R. Kelley

• Curated by eLife

  eLife Assessment

  This important study shows that self-supervised pretraining on related fungal genomes can substantially improve sequence-to-expression prediction in budding yeast. The evidence for the main conclusion is convincing, with careful comparisons to models trained from random initialization and clear gains on held-out expression data. The broader claims about the optimal evolutionary scope and transfer of regulatory grammar are less fully supported.

Reviewed by eLife

Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma

1. Olivia G Waltner
2. April A Apfelbaum
3. Emma D Wrenn
4. Shruti S Bhise
5. Sami B Kanaan
6. Rula Green Gladden
7. Mark A Mendoza
8. Roger Volden
9. Zev Kronenberg
10. Anand Patel
11. Michael Dyer
12. Jay F Sarthy
13. Elizabeth R Lawlor
14. Scott N Furlan

• Curated by eLife

  eLife Assessment

  This valuable study presents an analysis of the gene regulatory networks that contribute to tumour heterogeneity and tumor plasticity in Ewing sarcoma, with key implications for other fusion-driven sarcomas. The authors employed compelling orthogonal approaches, including single-cell sequencing and xenografts, to reveal the existence and plasticity of specific gene regulatory networks (e.g., TGF-beta signaling) within Ewing sarcoma, as well as significant differences that exist between cell lines and patient tumors.

Reviewed by eLife

Breaking the cold chain: solutions for room temperature preservation of mosquitoes leading to high quality reference genomes

1. Fiona Teltscher
2. Petra Korlević
3. Edel Sheerin
4. Alex Makunin
5. Mara K N Lawniczak

Reviewed by GigaScience

Systematic identification of oscillatory gene expression in single cell types

1. Alexis Weinreb
2. Manasa Basavaraju
3. Marc Hammarlund
4. Maxwell G. Heiman

Reviewed by Review Commons