Bioinformatics

Joint analysis of human retroelements-linked histone modification profiles reveals quickly evolving molecular processes connected with cancer

1. Daniil Nikitin

Reviewed by PREreview

Evidence of off-target probe binding affecting 10x Genomics Xenium gene panels compromise accuracy of spatial transcriptomic profiling

1. Caleb Hallinan
2. Hyun Joo Ji
3. Edmund Tsou
4. Steven L Salzberg
5. Jean Fan

• Curated by eLife

  eLife Assessment

  This valuable study identifies and characterizes probe binding errors in a widely used commercial platform for spatial transcriptomics, discovering that at least 21 out of 280 genes in a human breast cancer panel are not accurately detected. The authors provide convincing evidence for their findings through validation against multiple independent sequencing technologies and reference datasets, and they introduce a computational tool to help predict potential off-target probe binding. Given the broad adoption of this platform in biomedical research, this work provides an essential quality control resource that will improve data interpretation across numerous studies.

Reviewed by eLife

The Limitations of TabPFN for High-Dimensional RNA-seq Analysis

1. Summer Zhou
2. Vinayak Agarwal
3. Ashwin Gopinath
4. Timothy Kassis

Reviewed by Arcadia Science

Phylogenetic detection of protein sites associated with continuous traits

1. Louis Duchemin
2. Gerard Muntane Medina
3. Bastien Boussau
4. Philippe Veber

Reviewed by Arcadia Science

Label-free biochemical imaging and timepoint analysis of neural organoids via deep learning-enhanced Raman microspectroscopy

1. Dimitar Georgiev
2. Ruoxiao Xie
3. Daniel Reumann
4. Xiaoyu Zhao
5. Álvaro Fernández-Galiana
6. Mauricio Barahona
7. Molly M. Stevens

Reviewed by Arcadia Science

Leveraging AI to explore structural contexts of post-translational modifications in drug binding

1. Kirill E. Medvedev
2. R. Dustin Schaeffer
3. Nick V. Grishin

Reviewed by eLife

Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination

1. Aitor Zabala
2. Alex M. Ascensión
3. Iñigo Prada-Luengo
4. David Otaegui

Reviewed by GigaScience

TOGGLE Unveils Functional Heterogeneity and Epigenetic Memory in Single Cells

1. Junpeng Chen
2. Tianda Sun
3. Tian Song
4. Zhouweiyu Chen
5. Haowei Xu
6. Zixuan Guo
7. Eric Jiang
8. Yibing Nong
9. Tao Yuan
10. Charles C. Dai
11. Yexing Yan
12. Jinwen Ge
13. Haihui Wu
14. Tong Yang
15. Shanshan Wang
16. Zixiang Su
17. Park Tian
18. Xiao Yang
19. Ahmed Abdelbsset-Ismail
20. You Li
21. Changping Li
22. Richa A. Singhal
23. Kailin Yang
24. Lu Cai
25. Zixin Wu
26. Alex P. Carll

Reviewed by Review Commons

ProteomeLM: A proteome-scale language model enables accurate and rapid prediction of protein-protein interactions and gene essentiality across taxa

1. Cyril Malbranke
2. Gionata Paolo Zalaffi
3. Anne-Florence Bitbol

Reviewed by Arcadia Science

RAG-ESM: Improving pretrained protein language models via sequence retrieval

1. Damiano Sgarbossa
2. Anne-Florence Bitbol

Reviewed by Arcadia Science