Bioinformatics

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

Biophysics-based protein language models for protein engineering

1. Sam Gelman
2. Bryce Johnson
3. Chase Freschlin
4. Arnav Sharma
5. Sameer D’Costa
6. John Peters
7. Anthony Gitter
8. Philip A. Romero

Reviewed by Arcadia Science

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 LLMs 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

Drug combination prediction for cancer treatment using disease-specific drug response profiles and single-cell transcriptional signatures

1. Daniel Osorio
2. Parastoo Shahrouzi
3. Xavier Tekpli
4. Vessela N. Kristensen
5. Marieke L. Kuijjer

• Curated by eLife

  eLife Assessment

  This research addresses an important and timely topic in cancer treatment, as the authors present a novel computational tool, 'retriever,' which has the potential to revolutionize personalized cancer treatment strategies by predicting effective drug combinations for triple-negative breast cancer. The strength of the evidence presented is solid, as evidenced by the systematic testing of 152 drug response profiles and 11,476 drug combinations.

Reviewed by eLife