Bioinformatics

Distilling Structural Representations into Protein Sequence Models

1. Jeffrey Ouyang-Zhang
2. Chengyue Gong
3. Yue Zhao
4. Philipp Krähenbühl
5. Adam R. Klivans
6. Daniel J. Diaz

Reviewed by Arcadia Science

How Does Sampling Affect the AI Prediction Accuracy of Peptides’ Physicochemical Properties?

1. Meiru Yan
2. Ankeer Abuduhebaier
3. Haojin Zhou
4. Jiaqi Wang

Reviewed by PREreview

Permute-match tests: Detecting 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

Tidyplots empowers life scientists with easy code‐based data visualization

1. Jan Broder Engler

Reviewed by preLights

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