Bioinformatics

CryoNeRF: reconstruction of homogeneous and heterogeneous cryo-EM structures using neural radiance field

1. Huaizhi Qu
2. Xiao Wang
3. Yuanyuan Zhang
4. Sheng Wang
5. William Stafford Noble
6. Tianlong Chen

Reviewed by PREreview

Discovery of Novel Inhibitors of HMG-CoA Reductase using Bioactive Compounds isolated from Cochlospermum Species through Computational Methods

1. Toba Isaac Olatoye

Reviewed by PREreview

The inflammatory skin disease map (ISD map): an interactive computational resource focused on psoriasis and atopic dermatitis molecular mechanisms

1. Marcio L. Acencio
2. Oxana Lopata
3. Ahmed A. Hemedan
4. Nick Dand
5. Stephan Weidinger
6. Lavinia Paternoster
7. Sara J. Brown
8. Joseph Rastrick
9. Catherine H. Smith
10. Matthias Hübenthal
11. Ravi Ramessur
12. Matladi Ndlovu
13. Soumyabrata Ghosh
14. Xinhui Wang
15. Reinhard Schneider
16. Venkata Satagopam
17. Marek Ostaszewski

Reviewed by Arcadia Science

Exploring the repository of de novo-designed bifunctional antimicrobial peptides through deep learning

1. Ruihan Dong
2. Rongrong Liu
3. Ziyu Liu
4. Yangang Liu
5. Gaomei Zhao
6. Honglei Li
7. Shiyuan Hou
8. Xiaohan Ma
9. Huarui Kang
10. Jing Liu
11. Fei Guo
12. Ping Zhao
13. Junping Wang
14. Cheng Wang
15. Xingan Wu
16. Sheng Ye
17. Cheng Zhu

• Curated by eLife

  eLife Assessment

  This study presents a useful pipeline for de novo design of antimicrobial peptides active both against bacteria and viruses. The method is based on deep learning, using a GAN generator and a regression tasked to predict antimicrobial activity. The experimental evidence supporting the conclusions is solid, with 24 validated peptides, although some additional justifications of the computational strategy would be a plus. This work will be of interest to the community working on machine learning for biomedical applications and specifically on antimicrobial peptides.

Reviewed by eLife

xRead: a coverage-guided approach for scalable construction of read overlapping graph

1. Tangchao Kong
2. Yadong Wang
3. Bo Liu

Reviewed by GigaScience

TransHLA: A Hybrid Transformer Model for HLA-Presented Epitope Detection

1. Tianchi Lu
2. Xueying Wang
3. Wan Nie
4. Miaozhe Huo
5. Shuaicheng Li

Reviewed by GigaScience

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