Bioinformatics

DUAL: deep unsupervised simultaneous simulation and denoising for cryo-electron tomography

1. Xiangrui Zeng
2. Yizhe Ding
3. Yueqian Zhang
4. Mostofa Rafid Uddin
5. Ali Dabouei
6. Min Xu

• Curated by eLife

  eLife Assessment

  This important study presents a computational framework inspired by cycleGAN that enables denoising and realistic simulation of cryo-electron tomography data, addressing central challenges in tomogram cleaning, simulation, and downstream annotation. The approach coherently links several key problems in the field and demonstrates strong performance across benchmark datasets, with additional benefits for particle detection and missing-wedge completion, indicating broad relevance across electron tomography. The evidence is solid, with appropriate quantitative benchmarks and applications to diverse datasets supporting the main claims, although validation on additional, more recent tomograms would further strengthen the conclusions.

Reviewed by eLife

TSvelo: Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription and splicing

1. Jiachen Li
2. Zhe Wang
3. Hong-Bin Shen
4. Ye Yuan

• Curated by eLife

  eLife Assessment

  This study presents a valuable RNA velocity method which predicts the transcription rate linearly based on the expression of RNA levels of transcription factors with addition of comprehensive analyses. The evidence supporting the claims of the authors is solid, although inclusion of a full simulation would have strengthened the study. The work will be of interest to scientists working in the field of RNA biology and precision medicine.

Reviewed by eLife

Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions

1. Rémy Torro
2. Beatriz Díaz-Bello
3. Dalia El Arawi
4. Ksenija Dervanova
5. Lorna Ammer
6. Florian Dupuy
7. Patrick Chames
8. Kheya Sengupta
9. Laurent Limozin

• Curated by eLife

  eLife Assessment

  CellDetective is an important software package for segmentation, tracking, and analysis of time-lapse microscopy datasets, specifically designed to be accessible to researchers without coding expertise. The authors provide convincing evidence of its capabilities through comprehensive validations and well-executed comparisons across immunological assays, and the latest version adds support for defining and visualizing multiple cell subsets. The current implementation remains limited to 2D widefield imaging, though the authors provide a sound rationale for this scope, and one interface issue (a fixed main-window size on some systems) still affects usability. Overall, this work will be of significant interest to the bioimaging community, especially those in immunology and cell biology, and has applicability extending well beyond immune profiling.

Reviewed by eLife

TopoMetry systematically learns and evaluates the latent geometry of single-cell data

1. David Sidarta-Oliveira
2. Ana I Domingos
3. Licio A Velloso

• Curated by eLife

  eLife Assessment

  This important study presents a theoretically grounded framework for dimensionality reduction in single-cell RNA sequencing data, utilizing the principles of Riemannian manifolds. The proposed method addresses a critical challenge in bioinformatics-extracting highly informative latent dimensions without relying on the heuristic assumptions common in existing workflows. The evidence supporting the method's utility in estimating intrinsic dimensionality and identifying cell types is convincing, though the work would benefit from more rigorous validation against established ground truths and a clearer strategy for addressing prevalent batch effects.

Reviewed by eLife

TissueFormer: Extending single-cell foundation models to predict population-level phenotypes

1. Ari S. Benjamin
2. Anthony Zador

Reviewed by PREreview

Sample-level modeling of single-cell data at scale with tinydenseR

1. Pedro Milanez-Almeida
2. Daniela Schildknecht
3. Markus Linder
4. Saskia M. Brachmann
5. Andreas Weiss
6. Flavia Adler
7. Sofia Cardoni Lenticchia
8. Morgane Meistertzheim
9. Sophia Wild
10. Rachel Cuttat
11. Pushpa Jayaraman
12. Lang Ho Lee
13. Tanya Mulvey
14. Nadia Hassounah
15. Gina Crafts
16. David S. Quinn
17. Elena J. Orlando

Reviewed by Review Commons

Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2

1. Markus Hoffmann
2. Lina-Liv Willruth
3. Alexander Dietrich
4. Hye Kyung Lee
5. Ludwig Knabl
6. Nico Trummer
7. Jan Baumbach
8. Priscilla A. Furth
9. Lothar Hennighausen
10. Markus List

Reviewed by Rapid Reviews Infectious Diseases

Calibrated analysis framework for nanopore direct RNA sequencing uncovers cell-specific m6A stoichiometry at conserved sites

1. Denise Ohnezeit
2. Elene Loliashvili
3. Gregory Putzel
4. Ruth Verstraten
5. Jianheng Liu
6. Luke S Nicholson
7. Alejandro Pironti
8. Samie R Jaffrey
9. Daniel P Depledge
10. Angus C Wilson

• Curated by eLife

  eLife Assessment

  This valuable study compares orthogonal approaches for detecting RNA chemical modifications and provides a helpful framework for improving the reliability of direct RNA sequencing-based identification of RNA modifications. The evidence supporting the technical benchmarking claims is solid. However, support for the broader biological conclusions is not as strong, and the quantitative interpretation of the results, as well as the limitations of the underlying models, would benefit from further clarification.

Reviewed by eLife

GEfetch2R : fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools

1. Yabing Song
2. Jianbin Wang
3. Jiaxin Gao

Reviewed by GigaScience

HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets

1. Clara Arboleda-Baena
2. Felipe Borim Corrêa
3. João Pedro Saraiva
4. Santiago Castillo-Rivadeneira
5. Jonas Coelho Kasmanas
6. Antonis Chatzinotas
7.  Stephanie D Jurburg

Reviewed by GigaScience