Bioinformatics

Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats

1. Hong Yang
2. Cheng Zhang
3. Woonghee Kim
4. Mengnan Shi
5. Metin Kiliclioglu
6. Cemil Bayram
7. Ismail Bolar
8. Özlem Özdemir Tozlu
9. Cem Baba
10. Nursena Yuksel
11. Serkan Yildirim
12. Shazia Iqbal
13. Jihad Sebhaoui
14. Ahmet Hacımuftuoglu
15. Matthias Uhlen
16. Jan Boren
17. Hasan Turkez
18. Adil Mardinoglu

• Curated by eLife

  eLife Assessment

  The authors implement a valuable multi-tissue approach to dissect the physiologic consequences of JNK inhibition in parallel with dietary perturbation via sucrose. The conclusions of disrupted liver, muscle and adipose metabolism being central to these effects are solid, as they are supported by a combination of experimental dissection and network modeling approaches.

Reviewed by eLife

InterPLM: Discovering Interpretable Features in Protein Language Models via Sparse Autoencoders

1. Elana Simon
2. James Zou

Reviewed by PREreview

AACDB: Antigen-Antibody Complex Database — a Comprehensive Database Unlocking Insights into Interaction Interface

1. Yuwei Zhou
2. Wenwen Liu
3. Ziru Huang
4. Yushu Gou
5. Siqi Liu
6. Lixu Jiang
7. Yue Yang
8. Jian Huang

• Curated by eLife

  eLife Assessment

  This useful manuscript provides a newly curated database (termed AACDB) of antibody-antigens structural information, alongside annotations that are either taken and from the PDB, or added de-novo. Sequences, structures, and annotations can be easily downloaded from the AACDB website, speeding up the development of structure-based algorithms and analysis pipelines to characterize antibody-antigen interactions. The methodology presented for this data curation is solid, although some key annotations are missing which would greatly improve the database.

Reviewed by eLife

IMMClock reveals immune aging and T cell function at single-cell resolution

1. Yael Gurevich Schmidt
2. Di Wu
3. Sanna Madan
4. Sanju Sinha
5. Sahil Sahni
6. Vishaka Gopalan
7. Binbin Wang
8. Saugato Rahman Dhruba
9. Alejandro A. Schäffer
10. Nan-ping Weng
11. Nicholas P. Restifo
12. Kun Wang
13. Eytan Ruppin

Reviewed by preLights

PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure

1. Yongxin Ji
2. Jiayu Shang
3. Jiaojiao Guan
4. Wei Zou
5. Herui Liao
6. Xubo Tang
7. Yanni Sun

Reviewed by GigaScience

Benchmarking the coding strategies of non-coding mutations on sequence-based downstream tasks with machine learning

1. Zhe Liu
2. Yihang Bao
3. Wenhao Li
4. Weihao Li
5. Guan Nin Lin

Reviewed by Arcadia Science

The Effects of Nonlinear Signal on Expression-Based Prediction Performance

1. Benjamin J. Heil
2. Jake Crawford
3. Casey S. Greene

Reviewed by Arcadia Science, Review Commons

Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing

1. Matthew T. Parker
2. Samija Amar
3. José A. Campoy
4. Kristin Krause
5. Sergio Tusso
6. Magdalena Marek
7. Bruno Huettel
8. Korbinian Schneeberger

Reviewed by Review Commons

NeuroVar: an open-source tool for the visualization of gene expression and variation data for biomarkers of neurological diseases

1. Hiba Ben Aribi
2. Najla Abassi
3. Olaitan I. Awe

Reviewed by GigaByte

Binary Discriminator Facilitates GPT-based Protein Design

1. Zishuo Zeng
2. Rufang Xu
3. Jin Guo
4. Xiaozhou Luo

Reviewed by Arcadia Science