Bioinformatics

Untargeted pixel-by-pixel metabolite ratio imaging as a novel tool for biomedical discovery in mass spectrometry imaging

1. Huiyong Cheng
2. Dawson Miller
3. Nneka Southwell
4. Paola Porcari
5. Joshua L Fischer
6. Isobel Taylor
7. J Michael Salbaum
8. Claudia Kappen
9. Fenghua Hu
10. Cha Yang
11. Kayvan R Keshari
12. Steven S Gross
13. Marilena D'Aurelio
14. Qiuying Chen

• Curated by eLife

  eLife Assessment

  This valuable study describes a software package in R for visualizing metabolite ratio pairs. The evidence supporting the claims of the authors is solid and broadly supports the authors' conclusions. This work would be of interest to the mass spectrometry community.

Reviewed by eLife

Protein Language Model Fitness Is a Matter of Preference

1. Cade Gordon
2. Amy X. Lu
3. Pieter Abbeel

Reviewed by Arcadia Science

Protein Language Models Expose Viral Mimicry and Immune Escape

1. Dan Ofer
2. Michal Linial

Reviewed by Arcadia Science

ProtSpace: A Tool for Visualizing Protein Space

1. Tobias Senoner
2. Tobias Olenyi
3. Michael Heinzinger
4. Anton Spannagl
5. George Bouras
6. Burkhard Rost
7. Ivan Koludarov

Reviewed by Arcadia Science

Knowledge graph–based thought: a knowledge graph–enhanced LLM framework for pan-cancer question answering

1. Yichun Feng
2. Lu Zhou
3. Chao Ma
4. Yikai Zheng
5. Ruikun He
6. Yixue Li

Reviewed by GigaScience

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

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