Bioinformatics

NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing

1. Yuqian Liu
2. Zidong Su
3. Wenzhen Yang
4. Denghui Li
5. Jiawen Zhang
6. Yuning Zhang
7. Tao Zeng
8. Yong Zhang
9. Yuxiang Li
10. Guangyi Fan
11. Kailong Ma
12. Shanshan Liu
13. Xun Xu
14. Yuliang Dong
15. Zongan Wang

Reviewed by GigaScience

ScopeViewer: A Browser-Based Solution for Visualizing Spatial Transcriptomics Data

1. Danni Luo
2. Sophie Robertson
3. Yuanchun Zhan
4. Ruichen Rong
5. Shidan Wang
6. Xi Jiang
7. Sen Yang
8. Suzette Palmer
9. Liwei Jia
10. Qiwei Li
11. Guanghua Xiao
12. Xiaowei Zhan

Reviewed by GigaScience

ChatMDV: Democratising Bioinformatics Analysis Using Large Language Models

1. Maria Kiourlappou
2. Peter Todd
3. Yaxuan Kong
4. Jayesh Hire
5. Sibgathullah Furquan Nawab Mohammed
6. Martin Sergeant
7. Stefan Zohren
8. Jim Hughes
9. Stephen Taylor

Reviewed by GigaScience

CPSM: R-package of an Automated Machine Learning Pipeline for Predicting the Survival Probability of Single Cancer Patient

1. Harpreet Kaur
2. Pijush Das
3. Kevin Camphausen
4. Uma Shankavaram

Reviewed by GigaScience

Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity

1. Eric Greene
2. Richard Muniz
3. Hiroki Yamamura
4. Samuel E Hoff
5. Priyanka Bajaj
6. Markus CB Tecson
7. Cyrina Geluz
8. D John Lee
9. Erin M Thompson
10. Angelika Arada
11. Gyun Min Lee
12. Massimiliano Bonomi
13. Justin M Kollman
14. James S Fraser

• Curated by eLife

  eLife Assessment

  This manuscript employs cryo-EM, mutational analysis, and biochemical assays to explore the molecular basis by which glutamine promotes filamentation and regulates the activity of human glutamine synthetase (hGS) by stabilizing interactions between hGS decamers. The combined structural and biochemical data supporting the proposed mechanism are solid, although the evidence for a higher-order filamentous architecture and the precise assignment of the interface density would benefit from additional support. This work will be of particular interest and useful to groups interested in understanding the molecular basis of nutrient sensing, cellular metabolism, and structural regulation of enzyme activity.

Reviewed by eLife

Comprehensive RNA velocity by modeling the cascade of gene regulation, transcription, and splicing from single-cell RNA sequencing data with TSvelo

1. Jiachen Li
2. Zhe Wang
3. Hong-Bin Shen
4. Ye Yuan

• Curated by eLife

  eLife Assessment

  This study presents a valuable RNA velocity solution which integrates cell differentiation and gene regulation, with a balance between neuralODE and raw gene space. The evidence supporting the claims of the authors is solid, although inclusion of discussion on the challenges in capturing cell cycle transitions would have strengthened the study. The work will be of interest to scientists working in the field of computational biology and gene regulation.

Reviewed by eLife

Permute-match tests detect 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

PathoFact 2.0: An Integrative Pipeline for Predicting Antimicrobial Resistance Genes, Virulence Factors, Toxins and Biosynthetic Gene Clusters in Metagenomes

1. Júlia Ortís Sunyer
2. Luis F. Delgado
3. Oskar Hickl
4. Cedric C. Laczny
5. Patrick May
6. Paul Wilmes

Reviewed by GigaScience

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

1. Jia-Yuan Zhang
2. Changjiu Miao
3. Teng Qiu
4. Junyi He
5. Wenqi Cao
6. Wei Lin
7. Xiaoshuang Xia
8. Lei He
9. Chunlei Yang
10. Yuhui Sun
11. Tao Zeng
12. Yuxiang Li
13. Xun Xu
14. Yijun Ruan
15. Yuliang Dong

Reviewed by GigaScience

METRIN-KG: A knowledge graph integrating plant metabolites, traits, and biotic interactions

1. Disha Tandon
2. Tarcisio Mendes De Farias
3. Pierre-Marie Allard
4. Emmanuel Defossez

Reviewed by GigaScience