Bioinformatics

Miniature: Unsupervised glimpses into multiplexed tissue imaging datasets as thumbnails for data portals

1. Adam J Taylor

Reviewed by Arcadia Science

Protein Language Models Expose Viral Mimicry and Immune Escape

1. Dan Ofer
2. Michal Linial

Reviewed by Arcadia Science

AI-enabled Alkaline-resistant Evolution of Protein to Apply in Mass Production

1. Liqi Kang
2. Banghao Wu
3. Bingxin Zhou
4. Pan Tan
5. Yun (Kenneth) Kang
6. Yongzhen Yan
7. Yi Zong
8. Shuang Li
9. Zhuo Liu
10. Liang Hong

• Curated by eLife

  eLife Assessment

  This work presents a valuable exploration of AI-assisted protein engineering, particularly in designing a VHH antibody with enhanced resistance and stability to extreme environments. However, the approach is weakened by incomplete support, with computational methods and experimental design appearing somewhat arbitrary and lacking clear justification. Further justification of the chosen methods and clearer exposition would strengthen the study's support and conclusions.

Reviewed by eLife

Single-Cell and Spatial Transcriptomic Analyses Reveals the Dynamic Transcript Profiles of Myocardial Lymphangiogenesis post Myocardial Infarction

1. Jiaqi He
2. Dali Zhang
3. Haixu Song
4. Ziqi Liu
5. Dan Liu
6. Xiaolin Zhang
7. Xiaojie Zhao
8. Yan Zhang
9. Jing Liu
10. Jiaxin Xu
11. Chenghui Yan
12. Yaling Han

• Curated by eLife

  eLife Assessment

  This study presents useful albeit preliminary findings on transcriptome changes in cardiac lymphatic cells after myocardial infarction in mice. Despite revision, the conclusions of the authors remain uncertain as sample sizes in general are very low, and even sometimes too low to allow for valid statistical comparisons. Accordingly, there are concerns regarding statistical robustness, raised by both the editors and the reviewers. While the single-cell transcriptomic data were analyzed using solid advanced methodology, too few cells were included in the scRNA-seq data set and the spatial transcriptomics analyses. Thus, this study rather represents more a collection of preliminary transcriptomic data than a full scientific report that would definitively advance the field.

Reviewed by eLife

Statistical analysis supports pervasive RNA subcellular localization and alternative 3’ UTR regulation

1. Rob Bierman
2. Jui M. Dave
3. Daniel M. Greif
4. Julia Salzman

• Curated by eLife

  eLife assessment

  This paper describes an important, well-organized study into an under-exploited area of spatial transcriptomics. The limitations of the approach are generally made clear, but there is insufficient orthogonal validation to demonstrate the biological significance of the results, which leads to the evidence for the claims being currently incomplete. Nevertheless, the tools presented will provide a resource to researchers wishing to characterise spatial patterning of mRNAs, and the paper will be of interest to researchers studying cell biology, RNA biology, and method development for spatial transcriptomics/proteomics.

Reviewed by eLife

Identification of Potential Hub Genes and Therapeutic Targets in Colorectal Cancer Using Integrated Bioinformatics Approaches

1. Kamalakannan D
2. Manivannan R
3. Suresh Gopal Kumar
4. Dilip Kumar

Reviewed by PREreview

Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)

1. Seth A. Frazer
2. Mahdi Baghbanzadeh
3. Ali Rahnavard
4. Keith A. Crandall
5. Todd H. Oakley

Reviewed by GigaScience

CoCoPyE: feature engineering for learning and prediction of genome quality indices

1. Niklas Birth
2. Nicolina Leppich
3. Julia Schirmacher
4. Nina Andreae
5. Rasmus Steinkamp
6. Matthias Blanke
7. Peter Meinicke

Reviewed by GigaScience

spatiAlign: An Unsupervised Contrastive Learning Model for Data Integration of Spatially Resolved Transcriptomics

1. Chao Zhang
2. Lin Liu
3. Ying Zhang
4. Mei Li
5. Shuangsang Fang
6. Qiang Kang
7. Ao Chen
8. Xun Xu
9. Yong Zhang
10. Yuxiang Li

Reviewed by GigaScience

A data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence (MISIP)

1. Abigayle Simpson
2. Elisha M. Wood Charlson
3. Montana Smith
4. Kathleen Beilsmith
5. Ben Koch
6. Ramona L. Walls
7. Roland C. Wilhelm

Reviewed by GigaScience