Bioinformatics

Permute-match tests detect significant correlations between time series despite nonstationarity and limited replicates

1. Alex E Yuan
2. Wenying Shou

• Curated by eLife

  eLife Assessment

  This manuscript reports an important new statistical method for calculating the significance of correlations between two time-series, which provides more accuracy than other methods when the data has few replicates. The proposed method solves a real-life problem that is frequently encountered and is broadly applicable to many realistic datasets in many experimental contexts. The technique is supported with compelling mathematical derivations as well as analysis of both computer-generated and previously published experimental data.

Reviewed by eLife

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

1. Júlia Ortís Sunyer
2. Luis F. Delgado
3. Oskar Hickl
4. Cedric C. Laczny
5. Patrick May
6. Paul Wilmes

Reviewed by GigaScience

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

1. Jia-Yuan Zhang
2. Changjiu Miao
3. Teng Qiu
4. Junyi He
5. Wenqi Cao
6. Wei Lin
7. Xiaoshuang Xia
8. Lei He
9. Chunlei Yang
10. Yuhui Sun
11. Tao Zeng
12. Yuxiang Li
13. Xun Xu
14. Yijun Ruan
15. Yuliang Dong

Reviewed by GigaScience

METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions

1. Disha Tandon
2. Tarcisio Mendes De Farias
3. Pierre-Marie Allard
4. Emmanuel Defossez

Reviewed by GigaScience

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

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