Bioinformatics

Inferring protein from mRNA concentrations using convolutional neural networks

1. Patrick Maximilian Schwehn
2. Pascal Falter-Braun

Reviewed by preLights

In Silico Toxicity Assessment of Organophosphates: A DFT and Molecular Docking Study on Their Interaction with Human Serum Albumin (HSA)

1. Tanya Singh
2. Nisha Shankhwar
3. Neeta Raj Sharma
4. Anil Kumar
5. Awadhesh Kumar Verma

Reviewed by PREreview

On estimating phenomenological model states for epileptic seizure prediction

1. A I Bhatti

Reviewed by PREreview

Benchmarking Long-read Sequencing Tools for Chromosome End-specific Telomere Analysis

1. Jake Reed
2. Mark Oelkuct
3. Kevin Coombes

Reviewed by PREreview

Identification of Potential Hub Genes and Therapeutic Targets in Colorectal Cancer Using Integrated Bioinformatics Approaches

1. Kamalakannan D
2. Manivannan R
3. Suresh Gopal Kumar
4. Dilip Kumar

Reviewed by PREreview

CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics

1. Niema Moshiri

• Curated by GigaByte

  Editors Assessment:

  As volumes of viral and bacterial sequence data grow exponentially, the field of computational phylogenetics now demands resources to manage the burgeoning scale of this input data. This study introduces CompactTree, a C++ library designed for ultra-large phylogenetic trees with millions of tips. To address these scalability issues while maintaining ease of incorporation into external code bases, CompactTree is a header-only library with enhanced performance utilizing minimal dependencies, optimized node representation, and memory-efficient tree structure schemes. Resulting in significantly reduced memory footprints and improved processing times. Peer review requested some more detail on the functionality and some real-world examples, demonstrating the current utility of the tool. Although primarily supporting the (text-based) Newick format, the increased and extensibility scalability holds promise for multiple biological and epidemiological applications supporting more complex formats such as Nexus and NeXML. The tool is open source (GPLv3 licensed) and available in GitHub: https://niema.net/CompactTree

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

SqueezeCall: nanopore basecalling using a Squeezeformer network

1. Zhongxu Zhu

• Curated by GigaByte

  Editors Assessment:

  The accuracy of basecalling of nanopore sequencing still needs to be improved. With recent advances in deep learning this paper introduces SqueezeCall, a novel end-to-end tool for accurate basecalling. This uses Squeezeformer-achitecture which integrates local context extraction through convolutional layers and long-range dependency modeling via global context acquisition. Testing and peer review demonstrated that SqueezeCall outperformed traditional RNN and Transformer-based basecallers across multiple datasets, indicating its potential to refine genomic assembly and facilitate direct detection of modified bases in future genomic analytics. Future work is ongoing that will focus on training on highly curated datasets, including known modifications, to further increase research value. SqueezeCall is MIT licensed and available from GitHub here: https://github.com/labcbb/SqueezeCall

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Decoding the Molecular Language of Proteins with Evolla

1. Xibin Zhou
2. Chenchen Han
3. Yingqi Zhang
4. Huan Du
5. Jiayuan Tian
6. Jin Su
7. Renju Liu
8. Kai Zhuang
9. Shiyu Jiang
10. Anthony Gitter
11. Li Liu
12. Huayu Li
13. Meiqi Wu
14. Shiyang You
15. Zichen Yuan
16. Feng Ju
17. Huilin Zhang
18. Wei Zheng
19. Fengyuan Dai
20. Yuyang Zhou
21. Yuyang Tao
22. Dan Wu
23. Zongze Shao
24. Yang Liu
25. Hongyuan Lu
26. Fajie Yuan

Reviewed by preLights

Celldetective: an AI-enhanced image analysis tool for unraveling dynamic cell interactions

1. Rémy Torro
2. Beatriz Díaz-Bello
3. Dalia El Arawi
4. Ksenija Dervanova
5. Lorna Ammer
6. Florian Dupuy
7. Patrick Chames
8. Kheya Sengupta
9. Laurent Limozin

• Curated by eLife

  eLife Assessment

  CellDetective is a useful software package for segmentation, tracking, and analysis of time‐lapse microscopy datasets, specifically designed to be accessible to researchers without coding expertise. The authors provide solid evidence of its capabilities through comprehensive validations and well‐executed comparisons across immunological assays. However, the current implementation is limited to 2D widefield imaging and presents technical challenges - including occasional crashes, restricted flexibility in defining multiple cell populations, and some interface issues that hinder the full user experience. Overall, this work will be of significant interest to the bioimaging community, especially those in immunology and cell biology, and promises to evolve into a more robust tool with further development.

Reviewed by eLife

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